cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.fmhx98
title: Occurrence Download

description: A dataset containing 14711 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Adinetidae, Brachionidae, Gastropodidae, Dicranophoridae, Asplanchnidae, Euchlanidae, Proalidae, Notommatidae, Philodinidae, Collothecidae, Lepadellidae, Conochilidae, Trichocercidae, Epiphanidae, Trochosphaeridae, Flosculariidae, Habrotrochidae, Hexarthridae, Ituridae, Lecanidae, Lindiidae, Mytilinidae, Trichotriidae, Microcodidae, Philodinavidae, Synchaetidae, Testudinellidae, Scaridiidae, Tetrasiphonidae, Centropagidae, Diaptomidae, Cyclopidae, Halicyclopidae, Lernaeidae, Canthocamptidae, Ameiridae, Laophontidae, Phyllognathopodidae, Miraciidae, Ergasilidae, Daphniidae, Moinidae, Bosminidae, Chydoridae, Macrothricidae, Ilyocryptidae, Neothricidae)",
 "Geometry POLYGON ((-181.131592 -37.12775, -187.78141 -33.078885, -189.068184 -33.987495, -186.411552 -37.925243, -192.774353 -44.251839, -195.387383 -46.345032, -192.379532 -48.31083, -188.062592 -45.989329, -183.377609 -41.69727, -180.416107 -38.542795, -181.131592 -37.12775))"
 ]
}

 The dataset includes 14711 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000525-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.j4387
title: Data from: Triadic male-infant-male interaction serves in bond maintenance in male Assamese macaques

description: While the ultimate consequences of social bonds start to be better
 understood, the proximate behavioural mechanisms underlying the formation
 and maintenance of these close affiliative relationships have received
 less attention. We investigated the possible function of male-infant-male
 interactions (MIMIs) in male-male social bonding processes by analysing
 about 9000h of focal animal observations collected on two groups of wild
 Assamese macaques. In support of an agonistic buffering function of MIMIs,
 after engaging in a MIMI upon approach, subordinates stayed longer in
 close proximity of a dominant male. Overall, the frequency of MIMIs
 increased the stronger the affiliative relationship between two males,
 suggesting that MIMIs like grooming function in relationship maintenance.
 We did not find support for a role of MIMIs in bond formation as the
 frequency of MIMIs did not affect the time a male dyad spent in proximity
 in the consecutive year. Our results contribute to the general debate on
 behaviours influencing social dynamics in group living mammals.
description: Data_Triadic
 male-infant-male interaction serves in bond maintenance in male Assamese
 macaquesData_Model 1: MIMIs and
 time spent in close proximity after a subordinate male approached a more
 dominant male Data_Model 2: MIMIs and time spent in close proximity after
 a dominant male approached a subordinate male Data_Model 3: Effect of
 relationship strength on MIMI frequency Data_Model 4: Long-term effect of
 MIMI on future time spent in close proximity Data_Model 5: The effect of
 affiliative relationship strength on the MIMI rate of the consecutive
 year
DOI: 10.5061/dryad.pt180
title: Data from: Crossing the line: tunas actively exploit submesoscale fronts to enhance foraging success

description: Fronts – i.e., the boundaries between water masses – are ubiquitous in the
 world oceans and have been shown to significantly influence pelagic
 ecosystems with enhanced local productivity and increased abundances of
 forage fish and top predators. Here we use data from archival tags to
 document how four juvenile albacore tunas foraged at and exploited a
 thermal front. Of the 3,098 observed trips, the albacore mainly swam
 across the front between the warm side above the thermocline and the cold
 side below the thermocline with an average of 78 ± 20.4 cross-frontal
 trips per fish per day. The warm frontal surface waters provided a thermal
 resource, allowing the tuna to maintain higher body temperatures and thus
 forage more efficiently in the food-rich waters of the cold side of the
 front. Foraging success of the tunas decreased as the cross-front thermal
 gradient weakened. This first look into small-scale use of fronts by a top
 predator demonstrates that ephemeral, submesoscale oceanic features can
 play a significant role in pelagic ecology.
description: Snyder_etal_TunaAtFrontsMatlab workspace containing the archival tag data used in paper. The timeseries data is provided in a structure while the daily locations and their associated dates are provided in separate matrices. Each matrix has 4 columns which are associated with the four tags - the order of which is listed in the 'Front' structure. The 'Readme.m' file contains the code used to analyze this data.
DOI: 10.5061/dryad.sv8n7
title: Data from: Genetic assignment with isotopes and habitat suitability (GAIAH), a migratory bird case study

description: 1. Identifying migratory connections across the annual cycle is important
 for studies of migrant ecology, evolution, and conservation. While recent
 studies have demonstrated the utility of high-resolution SNP-based genetic
 markers for identifying population-specific migratory patterns, the
 accuracy of this approach relative to other intrinsic tagging techniques
 has not yet been assessed. 2. Here, using a straightforward application of
 Bayes' Rule, we develop a method for combining inferences from
 high-resolution genetic markers, stable isotopes, and habitat suitability
 models, to spatially infer the breeding origin of migrants captured
 anywhere along their migratory pathway. Using leave-one-out cross
 validation, we compare the accuracy of this combined approach with the
 accuracy attained using each source of data independently. 3. Our results
 indicate that when each method is considered in isolation, the accuracy of
 genetic assignments far exceeded that of assignments based on stable
 isotopes or habitat suitability models. However, our joint assignment
 method consistently resulted in small, but informative increases in
 accuracy and did help to correct misassignments based on genetic data
 alone. We demonstrate the utility of the combined method by identifying
 previously undetectable patterns in the timing of migration in a North
 American migratory songbird, the Wilson's warbler. 4. Overall, our
 results support the idea that while genetic data provides the most
 accurate method for tracking animals using intrinsic markers when each
 method is considered independently, there is value in combining all three
 methods. The resulting methods are provided as part of a new
 computationally-efficient R-package, GAIAH, allowing broad application of
 our statistical framework to other migratory animal systems.
description: Scripts needed to
 recreate all results.This is an Rstudio
 project with all necessary scripts for recreating all of our
 results.gaiah-wiwa-master.zipRstudio project with gaiah R packageThis is the source code for CRAN package gaiah version 0.0.2. It should not be necessary to use this, as you can just get the package from CRAN, but we include it here so as to have it archived.gaiah-master.zip
DOI: 10.5061/dryad.q8c13
title: Data from: Partitioning the effects of isolation by distance, environment, and physical barriers on genomic divergence between parapatric threespine stickleback

description: Genetic divergence between populations is shaped by a combination of
 drift, migration, and selection, yielding patterns of
 isolation-by-distance (IBD) and isolation-by-environment (IBE).
 Unfortunately, IBD and IBE may be confounded when comparing divergence
 across habitat boundaries. For instance, parapatric lake and stream
 threespine stickleback (Gasterosteus aculeatus) may have diverged due to
 selection against migrants (IBE), or mere spatial separation (IBD). To
 quantitatively partition the strength of IBE and IBD, we used
 recently-developed population genetic software (BEDASSLE) to analyze
 partial genomic data from three lake-stream clines on Vancouver Island. We
 find support for IBD within each of three outlet streams (unlike prior
 studies of lake-stream stickleback). In addition, we find evidence for IBE
 (controlling for geographic distance): the genetic effect of habitat is
 equivalent to geographic separation of ∼1.9km worth of IBD. Remarkably, of
 our three lake-stream pairs, IBE is strongest where migration between
 habitats is easiest. Such microgeographic genetic divergence would require
 exceptionally strong divergent selection, which multiple experiments have
 failed to detect. Instead, we propose that non-random dispersal (e.g.,
 habitat choice) contributes to IBE. Supporting this conclusion, we show
 that the few migrants between habitats are a non-random subset of the
 phenotype distribution of the source population.
description: Metadata_ComidaPhenotypic and geographic data for the Comida lake-stream pairMetadata_FarewellPhenotypic and geographic data for the Farewell lake-stream pair.Metadata_RobertsPhenotypic and geographic data for the Roberts lake-stream pair.ReadMe Weber_data_MorphDescription of the contents of the three Metadata files.Zip folder containing genotype dataThis is a Zip folder containing genotype data, SNP positional data within the genome, ecological and geographic and genetic distance matrices, and R code for BEDASSLE analyses.Bedassle_Data_Files_Evolution.zip
DOI: 10.5061/dryad.4nn26
title: Data from: Aboriginal and non-Aboriginal children in Western Australia carry different serotypes of pneumococci with different antimicrobial susceptibility profiles

description: Background: Carriage of Streptococcus pneumoniae is considered a precursor
 to pneumococcal diseases including pneumonia. As part of the Kalgoorlie
 Otitis Media Research Project, we characterised pneumococci isolated from
 the nasopharynx of Western Australian Aboriginal and non-Aboriginal
 children. Methods: Between 1999 and 2005, 100 Aboriginal and 180
 non-Aboriginal children were followed from birth to two years, with
 nasopharyngeal aspirates collected at ages 1–3 and 6–8 weeks, then at 4,
 6, 12, 18 and 24 months. Introduction of 7-valent pneumococcal conjugate
 vaccine (7vPCV) in 2001 enabled evaluation of its impact on carriage in
 study participants according to vaccines doses received. Pneumococcal
 serotyping was performed by Quellung and antimicrobial susceptibility by
 disk diffusion and Etest®. Molecular epidemiology of pneumococcal isolates
 was investigated by pulse-field gel electrophoresis and multilocus
 sequence typing. Results: Overall, the prevalence of 7vPCV serotypes was
 similar for Aboriginal and non-Aboriginal children (19 % vs. 16 %), but
 the prevalence of non-vaccine serotypes was higher in Aboriginal children
 (22 % vs. 7 %). A multi-resistant 6B clone (ST90) was found only in
 non-Aboriginal children. Aboriginal children who received three doses of
 7vPCV had lower odds of carrying 7vPCV serotypes (odds ratio [OR] 0.19, 95
 % CI 0.08–0.44) and higher odds of carrying non-vaccine serotypes (OR
 2.37, 95 % CI 1.13–4.99) than unvaccinated Aboriginal children; this
 finding was not observed in non-Aboriginal children. Conclusions: This
 unique study shows important differences in pneumococcal serotypes,
 genotypes, and antimicrobial susceptibility between Aboriginal and
 non-Aboriginal children living in the same geographic area before
 widespread 7vPCV use, and highlights the need for ongoing post-vaccination
 surveillance in outback Australia.
description: data file_micro results
 and vaccine status_17aug16Excel file for
 Streptococcus pneumoniae carriage isolates showing serotypes, molecular
 types, antimicrobial susceptibility, and date of collection. Information
 on the age, ethnicity, and pneumococcal conjugate vaccine status of study
 participants from whom the isolates were obtained is
 provided.data file for deposit_micro
 results and vaccine status_17aug16.xls
DOI: 10.15482/usda.adc/26800957
title: Data from: Prior sugarcane borer damage does not impact conspecific damage or perennial crop yield in subsequent years of growth

description: In perennial sugarcane (<i>Saccharum</i> spp.) agroecosystems, herbivory by lepidopteran stem borers like the sugarcane borer (SCB; <i>Diatraea saccharalis</i> (F.)) early in a growing season can increase the probability of conspecific herbivory later in the crop year. However, it is unknown if the effects of prior stem borer damage either to vegetatively propagated seed cane or standing plants can impact conspecific herbivory in ratoon growth following annual aboveground biomass harvest. Using the multiyear harvest cycle of Louisiana sugarcane, we conducted two field experiments and an analysis of a long-term dataset to evaluate if prior SCB damage increased levels of conspecific damage in subsequent crop years. In the first field study, we evaluated if SCB damage to whole stalk and billet seed cane decreased tiller emergence, aboveground biomass, fiber, and sucrose in the following two years of plant growth (i.e., plant cane and first ratoon). In the second field study, we evaluated the impacts of SCB damage sustained during different combinations of crop years on subsequent SCB damage and plant metrics as well as potential mechanisms mediating herbivore damage (i.e., nutrients and biological control potential). Finally, using a long-term dataset, we evaluated if SCB damage accrued during plant cane impacted the probability of conspecific damage in the first ratoon.
DOI: 10.15482/usda.adc/26800957.v1
title: Data from: Prior sugarcane borer damage does not impact conspecific damage or perennial crop yield in subsequent years of growth

description: In perennial sugarcane (<i>Saccharum</i> spp.) agroecosystems, herbivory by lepidopteran stem borers like the sugarcane borer (SCB; <i>Diatraea saccharalis</i> (F.)) early in a growing season can increase the probability of conspecific herbivory later in the crop year. However, it is unknown if the effects of prior stem borer damage either to vegetatively propagated seed cane or standing plants can impact conspecific herbivory in ratoon growth following annual aboveground biomass harvest. Using the multiyear harvest cycle of Louisiana sugarcane, we conducted two field experiments and an analysis of a long-term dataset to evaluate if prior SCB damage increased levels of conspecific damage in subsequent crop years. In the first field study, we evaluated if SCB damage to whole stalk and billet seed cane decreased tiller emergence, aboveground biomass, fiber, and sucrose in the following two years of plant growth (i.e., plant cane and first ratoon). In the second field study, we evaluated the impacts of SCB damage sustained during different combinations of crop years on subsequent SCB damage and plant metrics as well as potential mechanisms mediating herbivore damage (i.e., nutrients and biological control potential). Finally, using a long-term dataset, we evaluated if SCB damage accrued during plant cane impacted the probability of conspecific damage in the first ratoon.
DOI: 10.5061/dryad.vk8cd
title: Data from: Impact of habitat fragmentation on the spatial structure of the Eastern Arc Forests in East Africa: implications for biodiversity conservation

description: The Eastern Arc Mountains in Tanzania and Kenya are one of 35 global
 biodiversity hotspots. The Eastern Arc forests are, as are many other
 tropical biodiversity hotspots, highly fragmented. Understanding the
 impact of habitat fragmentation (i.e., habitat loss and subdivision) on
 the spatial structure of the Eastern Arc forests is important because
 forest spatial structure highly influences species richness, persistence,
 and extinction debt. Here we examine the impact of habitat fragmentation
 on the spatial structure of the Eastern Arc forests at a patch scale using
 very high resolution aerial imagery having a spatial resolution of 0.5–1.5
 m. Forest area across the 13 Eastern Arc Mountains is 405,852 ha and is
 distributed into 311 fragments ≥ 10 ha in size with a median fragment size
 of 84 ha. The 18 largest forest fragments in the Eastern Arc Mountains
 contain greater than three-quarters of total forest area. Average fragment
 isolation, as assessed by median distance to nearest fragment and median
 distance to the nearest larger fragment, is 867 and 1533 m, respectively.
 Of total forest area, 14% is &lt; 100 m from the forest edge and 33%
 is &lt; 300 m from the forest edge. Establishing forested linkages
 among the largest and closest forest fragments through forest regeneration
 and protection of secondary regenerating forest as well as providing
 protected area status to the remaining non-protected forest including
 unprotected smaller forest fragments are important to enhancing the
 long-term persistence of many plant and animal species here.
description: Shapes files of forest
 fragments in the Eastern Arc MountainsForest fragments
 containing native forest ≥10 ha in size and with ≥50% tree cover in 13
 Eastern Arc Mountains located in Tanzania and Kenya.AllFragments12272017_UTM.zip
DOI: 10.5061/dryad.7p5h6
title: Data from: Breeding synchrony and extrapair paternity in a species with alternative reproductive strategies

description: Breeding synchrony may affect the tradeoff between pursuing multiple mates
 and avoiding paternity loss, translating into differences in the rate of
 extrapair paternity (EPP). However, diverse empirical relationships
 between breeding synchrony and EPP remain challenging to explain. We
 examined whether the relationship between breeding synchrony and EPP
 varied with male morph, age, body size, or breeding density in the
 white-throated sparrow Zonotrichia albicollis. In this species, males of
 two genetically determined morphs pursue alternative mating strategies.
 Breeding synchrony positively correlated with EPP within polygamous white
 morph males, which have high rates of EPP and cuckoldry, but was unrelated
 to EPP within tan morph males, which prioritize mate guarding and paternal
 care. As previously reported, males that gained EPP were primarily white
 males. Males gained EPP more often than expected by chance during their
 mate’s fertile period and on neighboring territories. Since extrapair
 copulation appears primarily male-driven in this species, these results
 indicate that white males focus extra-pair mating effort during periods of
 high synchrony and during their mates’ fertile periods, even at the
 expense of paternity loss within their own nests. Breeding density, male
 age, and male size did not modify the relationship between breeding
 synchrony and EPP. However, older white males had higher cuckoldry rates,
 perhaps reflecting declines in performance associated with senescence.
 Results suggest that, even within species, mating strategy may modify how
 breeding synchrony affects rates of EPP, with positive relationships
 manifest only within subsets of individuals that pursue a strategy of
 polygyny at the expense of paternity loss.
description: Data for: Breeding
 synchrony and extrapair paternity in a species with alternative
 reproductive strategiesThis excel file contains
 information about the levels of extrapair paternity found in clutches of a
 polymorphic species, the white-throated sparrow (Zonotrichia albicollis).
 Levels of breeding synchrony are given for each clutch (nesting attempt).
 Each line contains data on one nestling, and nestlings are grouped into
 clutches. Information about male characteristics, breeding density, number
 of territorial neighbors, date, and clutch number (e.g., first or second
 nesting attempt) is also provided. PercentW is the proportion of the
 population consisting of white morph (versus the alternative tan morph)
 males.Grunst et al.
 2017_BreedingSynchronyEPC_WTSP.xls
DOI: 10.5061/dryad.1r0f7
title: Data from: Social learning of migratory performance

description: Successful bird migration can depend on individual learning, social
 learning, and innate navigation programs. Using 8 years of data on
 migrating whooping cranes, we were able to partition genetic and socially
 learned aspects of migration. Specifically, we analyzed data from a
 reintroduced population wherein all birds were captive bred and
 artificially trained by ultralight aircraft on their first lifetime
 migration. For subsequent migrations, in which birds fly individually or
 in groups but without ultralight escort, we found evidence of long-term
 social learning, but no effect of genetic relatedness on migratory
 performance. Social learning from older birds reduced deviations from a
 straight-line path, with 7 years of experience yielding a 38% improvement
 in migratory accuracy.
description: Distance of relocations
 to straight line pathdistanceToStraightLinePath.csvrelatedness
DOI: 10.5061/dryad.bb85640
title: Data from: Fern and lycophyte diversity in the Pacific Northwest: patterns and predictors

description: Recent floristic efforts in the Pacific Northwest (PNW) have made it
 possible to characterize the broad-scale patterns of fern and lycophyte
 diversity across this geologically-complex region of western North
 America. The physiography of the PNW has been developing for over 200
 million years, but Pleistocene glaciation-induced migrations and
 recolonizations have strongly influenced the assembly of the flora. With
 the high dispersal potential of spores, distribution patterns of
 pteridophytes may represent habitat suitability more than dispersal
 constraints. Our objective was to describe the biodiversity of
 pteridophytes in the PNW, determine the spatial distribution of that
 biodiversity in terms of phylogenetic diversity, identify centers of
 regional endemism, explore correlations between biodiversity and
 environmental variables, and infer influences of past glaciation on the
 pteridophyte flora. We obtained distribution data, constructed a
 phylogenetic tree using chloroplast data, and used the Biodiverse software
 package to estimate and map phylogenetic diversity and phylogenetic
 endemism across the PNW, identifying regions where diversity was higher or
 lower than expected in comparison to randomization models. Environmental
 correlates of diversity were identified using principal components
 analysis with bioclimatic data from WorldClim.org, and we used Maxent to
 predict habitat suitability for species under past and future climate
 conditions. We found evidence for the influence of glacial refugia on
 patterns of pteridophyte diversity, that moisture availability and cold
 temperatures are strongly correlated with patterns of richness,
 phylogenetic diversity, and phylogenetic endemism, and infer that
 topographic complexity may be driving the assembly of the pteridophyte
 flora indirectly by influencing climate and precipitation patterns.
description: Link-Perez_and_Laffan_2018_distribution-data_EPSG-4326Geographic coordinates (rounded to 0.001 decimal degrees) for the 32,012 georeferenced occurrence records used in the study. Data are provided in the original WGS84 (EPSG:4326) reference coordinate system.
DOI: 10.6084/m9.figshare.29578544
title: Datasets and Data dictionary for maternal Pf infection in the REVAMP trial

description: These datasets pertain to a study of Plasmodium falciparum infections prevalent in anaemic Malawian women participating in the REVAMP clinical trial (Pasricha, Lancet 2023).
DOI: 10.6084/m9.figshare.29578544.v1
title: Datasets and Data dictionary for maternal Pf infection in the REVAMP trial

description: These datasets pertain to a study of Plasmodium falciparum infections prevalent in anaemic Malawian women participating in the REVAMP clinical trial (Pasricha, Lancet 2023).