cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5068/d11974
title: Genomic approaches to mitigating genetic diversity loss in declining populations

description: The accelerating pace of global biodiversity loss is exacerbated by
 habitat fragmentation and subsequent inbreeding in small populations. To
 mitigate this issue, assisted breeding programs designed to protect small
 populations can be enhanced by incorporating genomic information. In this
 study, we use genomic tools to optimize genetic pairing in an assisted
 breeding program for a highly inbred population of Western burrowing owls.
 To maximize genetic diversity in the resulting offspring, we begin by
 creating an optimal pairing decision tree based on sex, kinship, and
 patterns of homozygosity across the genome. To evaluate the effectiveness
 of our strategy, we compare genetic diversity, brood size, and nestling
 success rates between optimized and non-optimized pairs. Additionally, we
 leverage recently discovered correlations between telomere length and
 fitness across species to investigate whether genomic optimization could
 have long-term fitness benefits. Our results indicate that pairing
 individuals with contrasting patterns of homozygosity across the genome is
 an effective way to increase genetic diversity in offspring. Although
 short-term field-based metrics of success did not differ significantly
 between optimized and non-optimized pairs, offspring from optimized pairs
 had significantly longer telomeres, suggesting that genetic optimization
 can help reduce the risk of inbreeding depression. These findings
 underscore the importance of genomic tools for increasing the
 effectiveness of assisted breeding programs and preserving the adaptive
 potential of small, inbred populations at risk of further decline.
DOI: 10.5061/dryad.b5mkkwhj2
title: Data from: Developmental rate displays effects of inheritance but not of sex in interpopulation hybrids of Tigriopus californicus

description: Coevolved genetic interactions within populations can be disrupted by
 hybridization resulting in loss of fitness in hybrid individuals (i.e.,
 hybrid breakdown). However, the extent to which variation in
 fitness-related traits among hybrids is inherited across generations
 remains unclear, and variation in these traits may be sex-specific in
 hybrids due to differential effects of genetic incompatibilities in
 females and males. Here we present two experiments investigating variation
 in developmental rate among reciprocal inter-population hybrids of the
 intertidal copepod Tigriopus californicus. Developmental rate is a
 fitness-related trait in this species that is affected by interactions
 between mitochondrial-encoded and nuclear-encoded genes in hybrids that
 result in variation in mitochondrial ATP synthesis capacities. First, we
 show that F2-hybrid developmental rate is equivalent in two reciprocal
 crosses and is unaffected by sex, suggesting that breakdown of
 developmental rate is likely experienced equally by females and males.
 Second, we demonstrate that variation in developmental rate among F3
 hybrids is heritable; times to copepodid metamorphosis of F4
 offspring of fast-developing F3 parents (12.25 ± 0.05 d, μ ± SEM) were
 significantly faster than those of F4 offspring of
 slow-developing parents (14.58 ± 0.05 d). Third, we find that ATP
 synthesis rates in these F4 hybrids are unaffected by the developmental
 rates of their parents, but that mitochondria from females synthesize ATP
 at faster rates than mitochondria from males. Taken together, these
 results suggest that sex-specific effects vary among fitness-related
 traits in these hybrids and that effects likely associated with hybrid
 breakdown display substantial inheritance across hybrid generations.
description: Developmental rate data – collected by daily monitoring of larval
 development (naupliar and copepodid) of individual <em>Tigriopus
 californicus</em> until either stage 1 copepodid metamorphosis was
 observed or adulthood was reached. ATP synthesis rate
 data – mitochondria isolated by differential centrifugation followed by in
 vitro assays of maximal ATP synthesis rate with saturating concentrations
 of substrates for either electron transport complex I or II.
description: All files are supplied as tab-delimited text files that can be
 opened with text editors, spreadsheets or R.
DOI: 10.5061/dryad.q2bvq83qq
title: Unexpected colour pattern variation in mimetic frogs: implication for the diversification of warning signals in the genus Ranitomeya

description: Predation is expected to promote uniformity in the warning colouration of
 defended prey, but also mimicry convergence between aposematic species.
 Despite selection constraining both colour-pattern and population
 divergence, many aposematic animals display numerous geographically
 structured populations with distinct warning signals. Here, we explore the
 extent of phenotypic variation of sympatric species of Ranitomeya poison
 frogs and test for theoretical expectations on variation and convergence
 in mimetic signals. We demonstrate that both warning signal and mimetic
 convergence are highly variable and are negatively correlated: some
 localities display high variability and no mimicry while in others the
 phenotype is fixed and mimicry is perfect. Moreover, variation in warning
 signals is always present within localities, and in many cases, this
 variation overlaps between populations, such that variation is continuous.
 Finally, we show that coloration is consistently the least variable
 element and is likely of greater importance for predator avoidance
 compared to patterning. We discuss the implications of our results in the
 context of warning signal diversification and suggest that, like many
 other locally adapted traits, a combination of standing genetic variation
 and founding effect might be sufficient to enable divergence in colour
 pattern.
DOI: 10.5061/dryad.k98sf7mc4
title: Temporal matches between monarch butterfly and milkweed population changes over the past 25,000 years

description: In intimate ecological interactions, the interdependency of species may
 result in correlated demographic histories. For species of conservation
 concern, understanding the long-term dynamics of such interactions may
 shed light on the drivers of population decline. Here we address the
 demographic history of the monarch butterfly, Danaus plexippus, and its
 dominant host plant, the common milkweed, Asclepias syriaca, using
 broad-scale sampling and genomic inference. Because genetic resources for
 milkweed have lagged behind those for monarchs, we first release a
 chromosome-level genome assembly and annotation for common milkweed. Next,
 we show that despite its enormous geographic range across eastern North
 America, A. syriaca is best characterized as a single, roughly panmictic
 population. Using Approximate Bayesian Computation via Random Forests
 (ABC-RF), a machine learning method for reconstructing demographic
 histories, we show that both monarchs and milkweed experienced population
 expansion during the most recent recession of North American glaciers
 10,000–20,000 years ago. Our data also identify concurrent population
 expansions in both species during the large-scale clearing of eastern
 forests (~200 years ago). Finally, we find no evidence that either species
 experienced a reduction in effective population size over the past 75
 years. Thus, the well-documented decline of monarch abundance over the
 past 40 years is not visible in our genomic dataset, reflecting a possible
 mismatch of the overwintering census population to effective population
 size in this species.
description: Scripts used in population genetic analyses; genomic data
 available on SRA.
DOI: 10.5061/dryad.9ghx3ffp3
title: Limestone spheroid 3D models for: The limestone spheroids of ‘Ubeidiya: Intentional imposition of symmetric geometry by early hominins?

description: Spheroids are one of the least understood lithic items yet are one of the
 most enduring, spanning from the Oldowan to the Middle Palaeolithic. Why
 and how they were made remains highly debated. We seek to address whether
 spheroids represent unintentional by-products of percussive tasks or if
 they were intentionally knapped tools with specific manufacturing goals.
 We apply novel 3D analysis methods, including spherical harmonics and
 surface curvature, to 150 limestone spheroids from ‘Ubeidiya (c.1.4Ma),
 presently the earliest Acheulean occurrence outside of Africa, to bring a
 new perspective to these enigmatic artefacts. We reconstruct the spheroid
 reduction sequence based on trends in their scar facets and geometry,
 finding that the spheroid makers at ‘Ubeidiya followed a premeditated
 reduction strategy. During their manufacture, the spheroids do not become
 smoother, but they become markedly more spherical. They approach an ideal
 sphere, a feat that likely required a mental template and skilful
 knapping. Acheulean bifaces are currently thought to represent the
 earliest evidence of hominins imposing a premeditated, symmetrical shape
 on stone. With evidence of spheroids occurring before the Acheulean, the
 intentional production of a sphere-like object now represents the oldest
 evidence of hominins desiring and achieving intentional geometry and
 symmetry in stone.
DOI: 10.5061/dryad.jdfn2z3g4
title: Data from: The role of fish feces for nutrient cycling on coral reefs

description: Consumers play an important role in biogeochemical cycles through the
 consumption and release of essential elements such as carbon (C), nitrogen
 (N), and phosphorus (P). Indeed, a large proportion of consumed elements
 are released into the environment in inorganic (i.e., excretion) or
 organic form (i.e., egestion). On coral reefs, fishes represent the bulk
 of consumer biomass and thus play a key role in the recycling of
 nutrients. In recent years, excretion rates have been studied intensively,
 but less is known about the rate and quality of coral reef fish egestion.
 In this study, we quantify the elemental contents of fish feces, estimate
 absorption efficiencies and compare egestion and excretion rates for 51
 coral reef fish species. We show that elemental concentrations decrease
 remarkably little from food to feces. This is due to extremely low
 absorption efficiencies, resulting in the egestion of large amounts of
 energy and nutrients. Moreover, we show that while the quality of fish
 feces varies across trophic guilds, it remains highly variable within
 trophic guilds. Finally, we demonstrate that the release of N and P
 through egestion outweighs the amount of nutrients recycled through
 excretion. Our study highlights the need to incorporate animal egestion
 into assessments of ecosystem functioning and food web structure.
description: Code to reproduce results presented in the manuscript can be
 found at GitHub.
DOI: 10.34810/data2706
title: Replication data for: Children’s gut microbiota predicts the efficacy of obesity treatment

description: This dataset compiles clinical and microbiological data from children diagnosed with obesity who participated in the Obemat 2.0 project. It includes gut microbial abundances obtained through the 16S rRNA sequencing method, 
along with calculated diversity indices and relevant clinical variables used in the associated study. 
These variables include the age, the metabolic risk score, BMI z-score, and changes in various cardiovascular risk factors throughout the intervention.
DOI: 10.25338/b8f075
title: Summary of SB 743 implementation efforts by California's 539 cities and counties

description: In 2013, then-Governor Jerry Brown signed Senate Bill (SB 743) into law.
 Pursuant to that direction, the Governor’s Office of Planning and Research
 (OPR) and the California Natural Resources Agency promulgated regulations
 and technical guidance that eliminated automobile level of service (LOS) –
 a measure of automobile delay – as a transportation impact metric for land
 development projects under the California Environmental Quality Act
 (CEQA), and replaced it with Vehicle Miles Traveled (VMT) – a measure of
 the amount of vehicular travel. Actual implementation of the LOS-to-VMT
 shift was left up to lead agencies—the agencies with primary approval
 authority over a given project, which for land development projects is
 usually leading a local government (city or county). Agencies were
 required to start using a VMT-based metric by July 1, 2020. Using LOS as
 the guiding metric for transportation impacts prioritizes vehicular flows
 and speed. As a result, it has had increasingly well-recognized
 consequences, including increasing the cost of infill development in urban
 areas (where roadways are typically more congested at baseline, making
 project-level transportation impacts more likely) and generally making the
 built environment more auto-centric. And many planners and policymakers
 viewed VMT as a more appropriate metric for achieving sustainability
 goals, like reduced greenhouse gas (GHG) emissions, improved public health
 and safety, and more streamlined infill development amidst California’s
 ongoing housing crisis. However, the LOS-to-VMT shift was also expected to
 create numerous challenges for transportation analysts, given the
 often-limited resources of local governments, the ingrained nature of LOS
 in transportation impact analyses, and the perceived lack of established
 practice with respect to VMT estimation, mitigation, and monitoring. With
 those concerns in mind, we undertook this study to investigate how local
 governments have been implementing the LOS-to-VMT shift for land
 development projects. We first explored whether and how local governments
 considered VMT impacts in CEQA analyses prior to the mandated change in
 transportation impact analysis metrics. We then used document review,
 direct outreach, and expert interviews to catalogue how each of
 California’s 539 cities and counties have responded to SB 743, focusing on
 jurisdictions’ acknowledgment of the policy shift, thresholds of VMT
 impact significance, VMT impact estimation methods (and tools), VMT impact
 mitigation guidance (and tools), VMT mitigation monitoring,
 inter-jurisdictional collaboration, continued use of LOS, and perceived
 effect of the LOS-to-VMT shift on land use development. The data set
 stored here summarizes our inventory findings. [1] LOS is generally
 assessed using six letter grades, from A (free flow) to F, which denote
 different levels of vehicular delay for intersections and different
 combinations of automobile speed, density, and capacity for roadway
 sections.
DOI: 10.5061/dryad.m905qfv6d
title: Inferring historical introgression with deep learning

description: Resolving the phylogenetic relationships among taxa remains a challenge in
 the era of big data due to the presence of genetic admixture in a wide
 range of organisms. Rapidly developing sequencing technologies and
 statistical tests enable evolutionary relationships to be disentangled at
 a genome-wide level, yet many of these tests are computationally intensive
 and rely on phased genotypes, large sample sizes, restricted phylogenetic
 topologies, or hypothesis testing. To overcome these difficulties, we
 developed a deep learning-based approach, named ERICA, for inferring
 genome-wide evolutionary relationships and local introgressed regions from
 sequence data. ERICA accepts sequence alignments of both population
 genomic data and multiple genome assemblies, and efficiently identifies
 discordant genealogy patterns and exchanged regions across genomes when
 compared with other methods. We further tested ERICA using real population
 genomic data from Heliconius butterflies that have undergone adaptive
 radiation and frequent hybridization. Finally, we applied ERICA to
 characterize hybridization and introgression in wild and cultivated rice,
 revealing the important role of introgression in rice domestication and
 adaptation. Taken together, our findings demonstrate that ERICA provides
 an effective method for teasing apart evolutionary relationships using
 whole genome data, which can ultimately facilitate evolutionary
 studies on hybridization and introgression.
DOI: 10.15468/dl.k5sa2f
title: Occurrence Download

description: A dataset containing 633944 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is France",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Larus argentatus"
 ]
}

 The dataset includes 633944 records from 1126 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003456-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dbrv15f64
title: Data for: Ingredient and nutrient composition of brown bear diets

description: The dietary nutrient profile has metabolic significance and possibly
 contributes to species’ foraging behavior. The brown bear (Ursus arctos)
 was used as a model species for which dietary ingredient and nutrient
 concentrations as well as nutrient ratios were determined annually,
 seasonally and per reproductive class. Brown bears had a vertebrate- and
 ant-dominated diet in spring and early summer and a berry-dominated diet
 in fall, which translated into protein-rich and carbohydrate-rich diets,
 respectively. Fiber concentrations appeared constant over time and
 averaged at 25 % of dry matter intake. Dietary ingredient proportions
 differed between reproductive classes; however, these differences did not
 translate into a difference in dietary nutrient concentrations, suggesting
 that bears manage to maintain similar nutrient profiles with selection of
 different ingredients. In terms of nutrient ratios, the dietary protein to
 non-protein ratio, considered optimal at around 0.2 (on metabolizable
 energy basis), averaged around 0.2 in this study in fall and around 0.8 in
 spring and summer. We introduced the minimal non-fat to fat ratio
 necessary for efficient maintenance metabolism. This ratio varied across
 seasons but never fell beneath the theoretically estimated minimum to
 ensure metabolic efficiency. This population thus managed to ingest diets
 that never exerted a lack of glucogenic substrate, suggesting that
 metabolic efficiency may either be a driver of active diet selection or
 that natural resources available to bears did not constitute a constraint
 in this respect. Given the considerable proportion of fiber in the diet of
 brown bears, the relevance of this nutrient and its role in foraging
 behavior might be underestimated.
description: Datapoints (fecal samples from GPS-tracked brown bears) were
 collected by the Scandinavian Brown Bear Research Project (this study:
 years 2015 to 2018). The estimated dietary content (EDC; ingredient
 composition of the 'ingested' diet) was calculated from fecal
 dietary remains (but see Hewitt and Robbins (1996)) for every fecal
 sample. The associated nutrient composition was calculated via a
 collection of literature data on nutrient composition of different dietary
 ingredients. The raw data on ingredient and nutrient composition of the
 brown bear diet were used to evaluate the annual and seasonal diet
 composition as well as the diet compostion per reproductive class.
 Nutrient ratio's were also calculated.
DOI: 10.5061/dryad.6hdr7sr5h
title: Ecological and life-history traits predict temporal trends in biomass of boreal moths

description:  Dramatic insect declines, and their consequences for ecosystems
 globally, have received considerable attention recently. Yet, it is still
 poorly known if ecological and life-history traits can explain declines
 and whether insect decline occurs also at high latitudes. Insects’
 diversity and abundance are dramatically lower at high latitudes compared
 to the tropics, and insects might benefit from climate warming in
 high-latitude environments.  We adopted a trait- and
 biomass-based approach to estimate temporal change between 1993 and 2019
 in Finnish macro-moth communities by using data from 85 long-running light
 traps. We analysed spatio-temporal variation in biomass of moth functional
 groups with Joint Dynamic Species Distribution Models while accounting for
 environmental variables.  We did not detect any declining trends
 in total moth biomass of moth functional groups, and most groups were
 stable over time. Moreover, biomass increased for species using coniferous
 trees, lichens, or mushrooms as hosts, multivoltine species, as well as
 monophagous and oligophagous species feeding on trees. We found that
 length and temperature of the growing season, winter climatic conditions,
 and habitat structure all partially explained variation in moth biomass.
 Although boreal moth communities are rapidly changing due to species
 turnover, in terms of total biomass they seem to contradict the trend of
 dramatic insect declines observed globally. This may lessen the immediate
 possibility of negative bottom-up trophic cascades in boreal food webs.
DOI: 10.25574/cdc.509
title: Chandra X-ray Observatory Chandra Data Collection for request #509

description: Chandra Data Collection for request #509
description: DOI updated to include the publication's DOI on 2026-01-28-10:00:00
DOI: 10.15468/dl.4vnn7r
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vachellia farnesiana",
 "Country is Micronesia (Federated States of)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024917-250811113504898/datasets/export for details.
DOI: 10.34740/kaggle/dsv/12813834
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.3bvj5b
title: Occurrence Download

description: A dataset containing 39 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vachellia farnesiana",
 "Country is El Salvador",
 "HasCoordinate is true"
 ]
}

 The dataset includes 39 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024916-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3jctth
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vachellia farnesiana",
 "Country is Fiji",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024919-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9kgebx
title: Occurrence Download

description: A dataset containing 1356 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Camellia sinensis"
 ]
}

 The dataset includes 1356 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010388-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.djuxjy
title: Occurrence Download

description: A dataset containing 92 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Otopappus imbricatus",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 92 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010389-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.