cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qz612jmb1
title: Direct and indirect effects of noise pollution alter biological communities in and near noise-exposed environments

description: Noise pollution is pervasive across every ecosystem on Earth. Although
 decades of research have documented a variety of negative impacts of noise
 to organisms, key gaps remain, such as how noise affects different taxa
 within a biological community and how effects of noise propagate across
 space. We experimentally applied traffic noise pollution to multiple
 roadless areas and quantified the impacts of noise on birds, grasshoppers,
 and odonates. We show that acoustically-oriented birds have reduced
 species richness and abundance and different community compositions in
 experimentally noise-exposed areas relative to comparable quiet locations.
 We also found both acoustically-oriented grasshoppers and odonates without
 acoustic receptors to have reduced species richness and/or abundance in
 relatively quiet areas that abut noise-exposed areas. These results
 suggest that noise pollution not only affects acoustically-oriented
 animals, but that noise may reverberate through biological communities
 through indirect effects to those with no clear links to the acoustic
 realm, even in adjacent quiet environments.
DOI: 10.5061/dryad.zkh18936r
title: Differential influence of Slc7a11 expression and body condition on pheomelanin‐based pigmentation in two Eurasian nuthatch Sitta europaea populations with different predation risk

description: The expression of the gene Slc7a11promotes the antioxidant
 capacity of cells by providing them with cysteine that can be used for the
 synthesis of glutathione (GSH), the most important intracellular
 antioxidant. In melanocytes, intracellular cysteine can also enter
 melanosomes and get incorporated in the pigment pheomelanin synthesis
 pathway, thus decreasing cysteine availability for GSH synthesis and
 potentially creating chronic oxidative stress. We thus hypothesized that a
 mechanism limiting the use of intramelanocytic cysteine for pheomelanin
 synthesis in environmental conditions generating oxidative stress may be
 physiologically advantageous and favored by natural selection. Here we
 searched for evidence of such a mechanism by comparing the influence of
 melanocytic Slc7a11expression on pheomelanin-based pigmentation
 in developing Eurasian nuthatch Sitta europaeanestlings from two
 populations differing in predation risk, a natural source of oxidative
 stress. Pheomelanin synthesis and pigmentation tended to increase
 with Slc7a11expression in the low-risk population as expected
 from the activity of this gene, but decreased
 with Slc7a11expression in the high-risk population. The same was
 not observed in the expression of five other genes influencing pheomelanin
 synthesis without affecting cysteine availability in melanocytes. The
 influence of body condition on the intensity of pheomelanin-based
 pigmentation also differed between populations, being positive in the
 low-risk population and negative in the high-risk population. The
 resulting pigmentation of birds was more intense in the high-risk
 population. These findings suggest that birds perceiving high predation
 risk may limit the use of cysteine for pheomelanin synthesis, which
 becomes independent of Slc7a11expression. Some birds may have
 thus evolved the ability to adjust their pigmentation phenotype
 to environmental stress.
description: See README file for further details
DOI: 10.5061/dryad.gxd2547gz
title: From Gondwana to GAARlandia: Evolutionary history and biogeography of ogre‐faced spiders (Deinopis)

description: Aim We explore the evolutionary history of the ogre‐faced spiders
 (Deinopis) from their Early Cretaceous origins to present day.
 Specifically, we investigate how vicariance and dispersal have shaped
 distribution patterns of this lineage. Within the Caribbean, we test the
 role of GAARlandia, a hypothesized land bridge that connected South
 America to the Greater Antilles during the Eocene–Oligocene transition
 (~35–33 Ma), in the biogeography of Deinopis. Taxon
 Araneae: Deinopidae: Deinopis. Location Caribbean islands, with
 additional global exemplars. Methods Combining standard Sanger sequence
 data with an Anchored Hybrid Enrichment (AHE) phylogenomic dataset, we use
 Bayesian inference to estimate the phylogenetic relationships
 of Deinopis. “BioGeoBEARS” is used to test the GAARlandia
 hypothesis, and to pinpoint major dispersal events in the biogeographic
 history of Deinopis. Results The phylogeny supports the nesting
 of a Caribbean clade within a continental grade. Model comparisons
 indicate GAARlandia as the best fitting model, and the biogeographic
 analyses reflect the geologic history within the Caribbean. Ancient and
 recent overwater dispersal events are also indicated within this lineage.
 There is also an ancient 113 Ma split into Old and New World
 clades. Main Conclusions The Deinopis phylogeny
 corresponds well with geography. This is reflected in the support for the
 GAARlandia land bridge hypothesis and the phylogenetic relationships
 within and among Caribbean islands mirroring nuances of Caribbean geologic
 history. Overwater dispersal also plays an important role in the
 biogeographic history of this lineage as implicated in the colonization of
 the volcanic and sedimentary Lesser Antilles and in a “reverse”
 colonization of North America. The spider family Deinopidae is an ancient
 lineage with origins dating back to Gondwana. While overwater dispersal
 has clearly played a role in the biogeography of the genus,
 the Deinopis phylogeny bears a strong signature of
 ancient geological events.
description: See README file for further instructions
DOI: 10.5066/p1i4rsar
title: Greatest-density regions for GPS locations of bison (Bos bison) at Badlands National Park, 2015-2024

description: This GIS shapefile, "density_contours," describes 1) a bison study area at Badlands National Park, South Dakota, and 2) 25%, 50%, 75%, and 99% kernel density contours for locations of bison marked with GPS collars during 2015-2024. Percentages associated with contours describe nominal coverage, i.e., proportions of observations they are expected to encompass, and approximate the distribution of bison activity within the study area. Each contour encompasses lower-coverage contours: the 75% contour, for example, encompasses the 50% and 25% contours but not the 99% contour. An accompanying child item, "quantile_bands," is a GIS shapefile that describes quantile bands corresponding with intervals between contours in "density_contours." Each of the first 4 bands encompasses approximately 25% of bison locations. Percentages associated with contours describe nominal coverage, i.e., quantiles the bands are expected to encompass. Bands comprise a partition of the bison study area and do not overlap. Users are advised that ground conditions within the study area may change over time, leading to changes in bison distribution.
DOI: 10.5061/dryad.q573n5tfg
title: Seasons of Syn

description: Synechococcus is a widespread and important marine primary
 producer. Time series provide critical information for identifying and
 understanding the factors that determine abundance patterns. Here, we
 present the results of analysis of a 16‐yr hourly time series
 of Synechococcus at the Martha's Vineyard Coastal
 Observatory, obtained with an automated, in situ flow cytometer. We focus
 on understanding seasonal abundance patterns by examining relationships
 between cell division rate, loss rate, cellular properties (e.g., cell
 volume, phycoerythrin fluorescence), and environmental variables (e.g.,
 temperature, light). We find that the drivers of cell division vary with
 season; cells are temperature‐limited in winter and spring, but
 light‐limited in the fall. Losses to the population also vary with season.
 Our results lead to testable hypotheses
 about Synechococcus ecophysiology and a working
 framework for understanding the seasonal controls
 of Synechococcus cell abundance in a temperate coastal
 system.
description: Data was collected and processed as described in Hunter-Cevera et
 al. 2019, Seasons of <em>Syn, Limnology and Oceanography.
 </em>Scripts used for data processing are available<em> at
 </em>http://github.com/hsosik/NES-LTER/tree/master/.
description: Data is organized into 3 tab-delimited text files:
 <strong>Synechococcus data and
 more:</strong><strong>
 </strong>lno2019_syn_temp_light.txt File includes
 daily values or averages of hourly data for: 
 <em>Synechococcus</em> cell concentration (cells
 per mL) estimates of division rate for
 <em>Synechococcus</em> population (per day)
 calculated loss rate from subtraction of net growth rate from
 division rate (per day) net growth rate calculated
 from day-to-day change in <em>Synechoocccus</em> cell
 concentration (per day) Minimum mode of cell volume
 (micrometer<sup>3</sup>) PE fluorescence
 at dawn PE fluorescence at dawn normalized by cell
 volume at dawn (1/micrometer<sup>3</sup>)
 Temperature (degree Celsius) Daily incident
 radiation (MJ/m<sup>2</sup>) 
 Missing data is denoted as NaNs.  
 <strong>Nutrient data:</strong>
 lno2019_nutrient_data.txt For available days, file
 includes: Concentration of nitrate+nitrite
 (microMolar) Concentration of ammonium
 (microMolar) Concentration of phosphate
 (microMolar) Concentration of silicate
 (microMolar) Values are means of 2-3
 technical replicates. Missing entries are denoted by NaNs.
   <strong>PAR attenuation
 coefficeint data:</strong>
 lno2019_attenuation_coefficients.txt For available
 days, file inlucdes: Station
 Latitude Station Longitude
 Attenuation coefficient (K) for PAR
 (meters<sup>-1</sup>) Please
 see corresponding paper for more details about data processing or
 corresponding scripts.
DOI: 10.5061/dryad.4mw6m9072
title: Data from: Siring success in kangaroos: size matters for those in the right place at the right time

description: In polygynous species, male reproductive success is predicted to be
 monopolized by a few dominant males. This prediction is often not
 supported, suggesting that ecological and alternative mating tactics
 influence siring success. The spatiotemporal distribution of individuals
 and the number of males competing for each receptive female are often
 overlooked, because they are difficult to monitor in wild animals. We
 examined how spatial overlap of female-male pairs, the time spent by a
 male on the breeding site, number of competitors and morphological traits
 influence siring probability in eastern grey kangaroos (Macropus
 giganteus). We compared home range overlap for 12,208 dam-male pairs and
 295 known dam-sire pairs to define local competitive groups and to
 estimate every male’s opportunity to sire the young of each female. We
 compared models considering morphological traits relative to the entire
 population or to local competitive groups. Including local competition
 improved model performance because it estimated the intensity of
 competition and compared each male’s morphological traits to those of its
 competitive group. Regardless of size, males can increase their
 probability to sire a young by increasing their mating opportunity
 relative to the mother. We underline the importance of considering spatial
 structure to assess the intensity of competition in species where males
 cannot equally access all females in a population. The estimation of
 mating opportunity and intensity of local competition improves our
 understanding of how morphological traits affect siring success when each
 mating event involves a different set of competing males, a characteristic
 of most wild species.
description: Data were collected at the Wilsons Promontory National Park
 (38°56’S, 146°17’E), Victoria, Australia.
description: Please see <strong>README_roo data.txt</strong> for
 details on variables found
 in <strong>data_roo_mating_opportunity.csv</strong>.
 The <strong>Mating_opportunity.R</strong> file
 includes the R script to estimate the mating opportunity of a male to mate
 with a specific female based overlap between their utilization
 distributions.
DOI: 10.6086/d1j383
title: Kinematic integration during prey capture varies among individuals but not ecological contexts in bluegill sunfish, Lepomis macrochirus (Perciformes: Centrarchidae)

description: The general ability for components of an organism to work together to
 achieve a common goal has been termed integration, and is often studied
 empirically by deconstructing organisms into component parts and
 quantifying covariation between them. Kinematic traits describing movement
 are useful for allowing organisms to respond to ecological contexts that
 vary on short time spans (milliseconds, minutes, etc.). Integration of
 these traits can contribute to maintaining whole-organism function, but it
 is unclear how modulation of component kinematic traits affects their
 integration. We examine integration of swimming and feeding during capture
 of alternative prey types in bluegill sunfish (Lepomis macrochirus).
 Despite the expected modulation of kinematics, integration within
 individuals was inflexible across prey types, suggesting functional
 redundancy for solving a broad constraint. However, integration was
 variable among individuals, suggesting that individuals vary in their
 solutions for achieving whole-organism function and this solution acts as
 a “top-down” regulator of component traits that adds insight into why
 kinematic variation is observed. Additionally, variation in kinematic
 integration among individuals could serve as a understudied target of
 environmental selection on prey capture, which is a necessary first step
 toward the observed divergence between populations and species.
description: Summary of data (variable definitions, etc.) included in first
 tab of Excel spreadsheet.
DOI: 10.5061/dryad.h18931zgr
title: Wild chimpanzees exhibit human-like aging of glucocorticoid regulation

description: Cortisol, a key product of the stress response, has critical influences on
 degenerative aging in humans. In turn, cortisol production is affected by
 senescence of the hypothalamic-pituitary-adrenal (HPA) axis, leading to
 progressive dysregulation and increased cortisol exposure. These processes
 have been studied extensively in industrialized settings, but few
 comparative data are available from humans and closely-related species
 living in natural environments, where stressors are very different. Here,
 we examine age-related changes in urinary cortisol in a 20-year
 longitudinal study of wild chimpanzees (N = 59 adults) in the Kanyawara
 community of Kibale National Park, Uganda. We tested for three key
 features of HPA aging identified in many human studies: increased average
 levels, a blunted diurnal rhythm, and enhanced response to stressors.
 Using linear mixed models, we found that aging was associated with a
 blunting of the diurnal rhythm and a significant linear increase in
 cortisol, even after controlling for changes in dominance rank. These
 effects did not differ by sex. Aging did not increase sensitivity to
 energetic stress or social status. Female chimpanzees experienced their
 highest levels of cortisol during cycling (versus lactation), and this
 effect increased with age. Male chimpanzees experienced their highest
 levels when exposed to sexually-attractive females, but this effect was
 diminished by age. Our results indicate that chimpanzees share some key
 features of HPA aging with humans. These findings suggest that impairments
 of HPA regulation are intrinsic to the aging process in hominids and are
 neither side effects of extended human lifespan nor of atypical
 environments.
DOI: 10.5061/dryad.jwstqjq5s
title: Conditional female strategies influence hatching success in a communally-nesting iguana

description: The decision of females to
 nest communally has important consequences for
 reproductive success. While often associated
 with reduced energetic expenditure, conspecific
 aggregations also expose females
 and offspring to conspecific
 aggression, exploitation, and
 infanticide. Intrasexual competition pressures
 areexpected to favor the evolution of conditional
 strategies, which could be based on simple decision
 rules (i.e., availability of nesting sites,
 synchronicity with conspecifics) or on a focal
 individual’s condition or status (i.e., body
 size). Oviparous reptiles that reproduce
 seasonally and provide limited to no
 postnatal care provide ideal
 systems for disentangling social factors that influence different female reproductive tactics from those present in offspring-rearing environments. In this study, we investigated whether nesting strategies in a West Indian rock iguana, Cyclura nubila caymanensis, vary conditionally with reproductive timing or body size, and evaluated consequences for nesting success. Nesting surveys were conducted on Little Cayman, Cayman Islands, British West Indies for four consecutive years. Use of high-density nesting sites was increasingly favored up to seasonal nesting activity peaks, after which nesting was generally restricted to low-density nesting areas. Although larger females were not more likely than smaller females to nest in high-density areas, larger females nested earlier and gained access to priority oviposition sites. Smaller females constructed nests later in the season, apparently foregoing investment in extended nest defense. Late-season nests were also constructed at shallower depths and exhibited shorter incubation periods. While nest depth and incubation length had significant effects on reproductive outcomes, so did local nest densities. Higher densities were associated with significant declines in hatching success, with up to 20% of egg-filled nests experiencing later intrusion by a conspecific. Despite these risks, nests in high-density areas were significantly more successful than elsewhere due to the benefits of greater chamber depths and longer incubation times. These results imply that communal nest sites convey honest signals of habitat quality, but that gaining and defending priority oviposition sites requires competitive ability.
description: These data were collected by observational and capture records of
 Cyclura nubila caymanensis on Little Cayman, Cayman Islands, as described
 in Materials and Methods and accompanying Appendices.
DOI: 10.5061/dryad.931zcrjgj
title: Generation of a chromosome-scale genome assembly of the insect-repellant terpenoid-producing Lamiaceae species, Callicarpa americana

description: Background: Plants exhibit wide chemical diversity due to production of
 specialized metabolites which function as pollinator attractants,
 defensive compounds, and signaling molecules. Lamiaceae (mints) are known
 for their chemodiversity and have been cultivated for use as culinary
 herbs and as sources of insect repellents, health-promoting compounds, and
 fragrance.  Findings: We report the chromosome-scale genome
 assembly of Callicarpa americana L. (American beautyberry), a species
 within the early diverging Callicarpoideae clade of the Lamiaceae, known
 for its metallic purple fruits and use as an insect repellent due to its
 production of terpenoids. Using long reads and Hi-C scaffolding, we
 generated a 506.1 Mb assembly spanning 17 pseudomolecules with an N50
 contig and N50 scaffold size of 7.5 Mb and 29.0 Mb, respectively. A total
 of 32,164 genes was annotated including 53 candidate terpene synthases and
 47 putative clusters of specialized metabolite biosynthetic pathways.
 Whole genome duplication analyses revealed three putative events, which
 together with local tandem duplication events, contributed to gene family
 expa, American beautyberransion of terpene synthases. Kolavenyl
 diphosphate is a gateway to many of C. americana’s bioactive terpenoids;
 experimental validation confirmed that CamTPS2 encodes kolavenyl
 diphosphate synthase. Syntenic analyses with Tectona grandis L. f. (teak),
 a member of the Tectonoideae clade of Lamiaceae known for exceptionally
 strong wood resistant to insects, revealed 963 collinear blocks and 21,297
 C. americana syntelogs. Conclusions: Access to the C. americana genome
 provides a roadmap for rapid discovery of genes encoding plant-derived
 agrichemicals and a key resource to understand the evolution of chemical
 diversity in Lamiaceae.
DOI: 10.5061/dryad.sbcc2fr32
title: Extinction dynamics under extreme conservation threat: The flora of St. Helena

description: The flora of the island of St Helena provides an amplified system for the
 study of extinction by reason of the island’s high endemism, small size,
 vulnerable biota, length of time of severe disturbance (since 1502), and
 severity of threats. Endemic plants have been eliminated from 96.5% of St
 Helena by habitat loss. There have been eight recorded extinctions in the
 vascular flora since 1771 giving an extinction rate of 581 extinctions per
 million species per year (E/MSY). This is considerably higher than
 background extinction rates, variously estimated at 1 or 0.1 E/MSY. We
 have no information for plant extinctions prior to 1771 but applying the
 same extinction rate to the period 1502 to 1771 suggests that there may be
 around ten unrecorded historical extinctions. We use census data and
 population decline estimates to project likely extinction forward in time.
 The projected overall extinction rate for the next 200 years is somewhat
 higher at 625 E/MSY. However, our data predict an extinction crunch in the
 next 50 years with 4 species out of the remaining 48 likely to become
 extinct during this period. It is interesting that during a period when
 the native plant areas dropped to 3.5% of the original, the extinction
 rate appears to have remained shallowly linear with under 30% of the
 endemic flora becoming extinct.
description: The time to percent decline (TPD)
 figures (see above) were standardized by conversion to half-lives (time to
 50% decline: TPD50) using a simple exponential function, i.e.
 t<sub>1/2</sub>=t/log<sub>1/2</sub>(N<sub>t</sub>/N<sub>0</sub>), where t<sub>1/2</sub>is the half-life (TPD50), t is the time period over which population decline has been measured, and N<sub>t</sub>/N<sub>0</sub>is the proportion of the population remaining after t. We use the exponential for the decline curves as this is a very common general form of decline curve (Di Fonzo et al., 2013). The TPD50 for a species is therefore assumed to be constant, following an exponential decay process. The TPD50 was then used in combination with the total number of mature individuals (NMI) to project changes in NMI forward in time. Under this simple model, plants are taken as extinct when NMI &lt;1.