cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5mkkwh72j
title: Data from: Phylogeography of the Cran’s bully Gobiomorphus basalis (Gobiiformes: Eleotridae) and an analysis of species boundaries within the New Zealand radiation of Gobiomorphus

description: New Zealand has a complex recent history of climatic and tectonic change
 that has left variable signatures in the geographic distribution and
 genetic structure of the region’s flora and fauna. To identify concordant
 patterns, a broad range of taxa must be examined and compared. In New
 Zealand’s North Island, a consensus is forming as to the dominant
 biogeographic barriers in the region although obligate freshwater taxa
 have not been considered in this framework. We use single-nucleotide
 polymorphisms to investigate phylogeography in the widespread obligate
 freshwater fish Gobiomorphus basalis on the North Island. Phylogeographic
 patterns within G. basalis reveal biogeographic disjunctions that are in
 some ways consistent and in other ways at odds with established patterns,
 providing insight into the processes that have shaped the islands’
 biogeography. We also use phylogeography to delineate species boundaries
 within the entire New Zealand radiation of Gobiomorphus and find that it
 contains several morphologically cryptic species. We resolve two clades
 within G. basalis that correspond to areas north and south of the Taupo
 Volcanic Zone. We confirm the distinctiveness of G. alpinus relative to G.
 cotidianus, as well as the presence of two lineages within G. breviceps
 that were previously identified based on mitochondrial data.
description: Report_DGobi19-4142_1_moreOrders_SNP_2 SNP
 dataset (DArTSeq) provided by Diversity Arrays Technology in 2-Row format
 (refer to https://www.diversityarrays.com/ for further information on data
 formats)
 <strong>Gobiomorphus_header</strong>
 Sample names and species designations to be read in with
 'Report_DGobi19-4142_1_moreOrders_SNP_2'
 <strong>Metadata</strong> Metadata
 info for dataset   See 'Gruber
 B, Unmack PJ, Berry OF, Georges A (2019) Introduction to dartR. User
 Manual' for details on how to manipulate this dataset.
DOI: 10.5061/dryad.xsj3tx9bp
title: Data from: Male phenotypes in a female framework: evidence for degeneration in sperm produced by male snails from asexual lineages

description: How changes in selective regimes affect trait evolution is an important
 open biological question. We take advantage of naturally occurring and
 repeated transitions from sexual to asexual reproduction in a New Zealand
 freshwater snail species, Potamopyrgus antipodarum, to address how
 evolution in an asexual content— including the potential for relaxed
 selection on male-specific traits— influences sperm morphology. The
 occasional production of male offspring by the otherwise all-female
 asexual P. antipodarum lineages affords a unique and powerful opportunity
 to assess the fate of sperm traits in a context where males are
 exceedingly rare. These comparisons revealed that the sperm produced by
 "asexual" males are markedly distinct from sexual counterparts.
 We also found that the asexual male sperm harbored markedly higher
 phenotypic variation and was much more likely to be morphologically
 abnormal. Together, these data suggest that transitions to asexual
 reproduction might be irreversible, at least in part because male function
 is likely to be compromised. These results are also consistent with a
 scenario where relaxed selection and/or mutation accumulation in the
 absence of sex translates into rapid trait degeneration.
DOI: 10.5061/dryad.5dv41ns3g
title: Data from: Resistance to gapeworm parasite has both additive and dominant genetic components in house sparrows, with evolutionary consequences for ability to respond to parasite challenge

description: Host parasite relationships are likely to change over the coming decades
 in response to climate change and increased anthropogenic stressors.
 Understanding the genetic architecture of parasite resistance will aid
 prediction of species’ responses to intensified parasite challenge. The
 gapeworm “Syngamus trachea” is prevalent in natural bird populations and
 causes symptomatic infections ranging from mild to severe. The parasite
 may affect ecological processes by curtailing bird populations and is
 important due to its propensity to spread to commercially farmed birds.
 Our large scale dataset on an insular house sparrow metapopulation in
 northern Norway includes information on gapeworm prevalence and infection
 intensity, allowing assessment of the genetics of parasite resistance in a
 natural system. To determine whether parasite resistance has a heritable
 genetic component, we performed variance component analyses using animal
 models. Resistance to gapeworm had substantial additive genetic and
 dominance variance, and genome wide association studies to identify SNPs
 associated with gapeworm resistance yielded multiple loci linked to immune
 function. Together with genome partitioning results, this indicates that
 resistance to gapeworm is under polygenic control in the house sparrow,
 and likely in other bird species. Hence, our results provide the
 foundation needed to study any eco-evolutionary processes related to
 gapeworm infection, and show that it is necessary to use methods suitable
 for polygenic and non-additive genetic effects on the phenotype.
DOI: 10.15468/dl.vgjq3w
title: Occurrence Download

description: A dataset containing 1586 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((159.00094 -48.95058,200.03306 -48.95058,200.03306 -32.54476,159.00094 -32.54476,159.00094 -48.95058))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Hypnum cupressiforme"
 ]
}

 The dataset includes 1586 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002311-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4tmpg4f6f
title: Phenotypic plasticity and community composition interactively shape trophic interactions

description: Trait variation defines and underpins biodiversity, yet we are only
 beginning to understand how processes acting across biological scales
 (individuals to whole communities) interact to produce trait differences
 and their consequences, particularly over short time scales. First,
 species often differ widely in their mean phenotype, meaning that changes
 in community composition can alter average trait values of a guild.
 Second, phenotypic plasticity alters the trait values of individuals, and
 the net effect of plasticity can also shift the average trait values of a
 specific species or of whole communities. However, community assembly,
 phenotypic plasticity, and their effects on biological patterns are not
 independent. The expression of phenotypic plasticity tends to be
 species-specific, meaning that differences in species’ relative abundances
 will shape trait change and resulting ecological patterns and processes. I
 test this idea using mesocosms and simulations of communities of dragonfly
 larvae that differ in activity rate. Some but not all species reduced
 their activity rate in response to predation risk, causing larger
 trait-mediated changes in trophic interactions in experimental communities
 dominated by plastic versus aplastic species. Using surveys and
 simulations of natural ponds, I demonstrate that community composition
 will shape patterns of phenotypic plasticity, with likely consequences for
 ecological dynamics in the wild. The interactive effects of trait
 differences across scales of biological organization necessitates an
 integrated view of diverse biological processes, including plasticity and
 community assembly, in order to understand ecological interactions.
DOI: 10.5061/dryad.mkkwh70wf
title: Genetic diversity and population structure in Chrysolepis chrysophylla (golden chinquapin; Fagaceae): SSRs vs SNPs

description: Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP)
 genotypes on the same plant samples of Chrysolepis chrysophylla (Fagaceae;
 golden chinquapin) from 22 sites were used to determine genetic diversity
 and population structure. One site of C. sempervirens allowed
 interspecific vs. intraspecific comparison. SSRs and SNPs yielded many
 similar results. Among-site variation contributed 13% to 17% of the
 genetic variation and Fst estimates of 0.14 to 0.17 were in the range
 expected among Fagaceae species rather than among populations within a
 species. The northern sites tended to group separately on the first two
 axes of multivariate scatterplots from southern sites. Sites in two
 geographically isolated areas were divergent: 1) the Hood Canal,
 Washington population was relatively more genetically distant from other
 golden chinquapin sites than was our C. sempervirens site; 2) three
 coastal southern California sites were moderately diverged. The Hood Canal
 site had a negative inbreeding coefficient, fewer alleles, lower
 heterozygosity, and differed from the Skamania County, Washington site as
 well as all other sites. Hood Canal trees are distinguished by disjunct
 geography and by these molecular results. This suggests that the golden
 chinquapin near Hood Canal be treated as a management unit, and potential
 conservation actions are discussed.
DOI: 10.5061/dryad.5qfttdz26
title: Data from: It takes two: heritable male effects on reproductive timing but not clutch size in a wild bird population

description: Within-population variation in the traits underpinning reproductive output
 has long been of central interest to biologists. Since they are strongly
 linked to lifetime reproductive success, these traits are expected to be
 subject to strong selection and, if heritable, to evolve. Despite the
 formation of durable pair bonds in many animal taxa, reproductive traits
 are often regarded as female-specific, and estimates of quantitative
 genetic variation seldom consider a potential role for heritable male
 effects. Yet reliable estimates of such social genetic effects are
 important since they influence the amount of heritable variation available
 to selection. Based on a 52-year study of a nestbox-breeding great tit
 (Parus major) population, we apply ‘extended’ bivariate animal models in
 which the heritable effects of both sexes are modelled to assess the
 extent to which males contribute to heritable variation in seasonal
 reproductive timing (egg laying date) and clutch size, while accommodating
 the covariance between the two traits. Our analyses show that reproductive
 timing is a jointly expressed trait in this species, with (positively
 covarying) heritable variation for laydate being expressed in both members
 of a breeding pair, such that the total heritable variance is 50% larger
 than estimated by traditional models. This result was robust to explicit
 consideration of a potential male-biased environmental confound arising
 through sexually dimorphic dispersal. In contrast to laydate, males’
 contribution to heritable variation in clutch size was limited. Our study
 thus highlights the contrasting extent of social determination for two
 major components of annual reproductive success, and emphasises the need
 to consider the social context of what are often considered
 individual-level traits.
description: See README.txt
DOI: 10.15468/dl.guawmy
title: Occurrence Download

description: A dataset containing 220 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Portugal",
 "TaxonKey is Felis silvestris"
 ]
}

 The dataset includes 220 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002310-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.qnk98sfcs
title: Data from: Separation of realized ecological niche axes among sympatric tilefishes provides insight into potential drivers of co‐occurrence in the NW Atlantic

description: Golden and Blueline Tilefish (Lopholatilus
 chamaeleonticeps and Caulolatilus microps) are keystone
 taxa in northwest (NW) Atlantic continental shelf‐edge environments due to
 their biotic (trophic‐mediated) and abiotic (ecosystem engineering)
 functional roles combined with high‐value fisheries. Despite this
 importance, the ecological niche dynamics (i.e., those relating to trophic
 behavior and food‐web interactions) of these sympatric species are poorly
 understood, knowledge of which may be consequential for maintaining both
 ecosystem function and fishery sustainability. We used stable isotope
 ratios of carbon (δ13C) and nitrogen (δ15N) to build realized ecological
 niche hypervolumes to serve as proxies for diet and production use
 patterns
 of L. chamaeleonticeps and C. microps. We hypothesized that: (a) species exhibit ontogenetic shifts in diet and use of production sources; (b) species acquire energy from spatially distinct resource pools that reflect a sedentary life‐history and differential use of the continental shelf‐edge; and (c) species exhibit differentiation in one or more measured niche axes. We found evidence for ontogenetic shifts in diet (δ15N) but not production source (δ13C) in both species, suggesting a subtle expansion of measured ecological niche axes. Spatial interpolation of stable isotope ratios showed distinct latitudinal gradients; for example, individuals were 13C enriched in northern and 15N enriched in southern regions, supporting the assertion that tilefish species acquire energy from regional resource pools. High isotopic overlap was observed among species (≥82%); however, when hypervolumes included depth and region of capture, overlap among species substantially decreased to overlap estimates of 15%–77%. This suggests that spatial segregation could alleviate potential competition for resources among tilefish species inhabiting continental shelf‐edge environments. Importantly, our results question the consensus interpretation of isotopic overlap estimates as representative of direct competition among species for shared resources or habitats, instead of identifying habitat segregation as a possible mechanism for the coexistence of tilefish species in the NW Atlantic.
DOI: 10.5061/dryad.612jm640w
title: Data from: Multi-generational genetic consequences of reinforcement in a bird metapopulation

description: Translocation of conspecific individuals to reduce extinction risk of
 small, isolated populations and prevent genetic depletion is a powerful
 tool in conservation biology. An important question is how the
 translocated individuals influence the long-term genetic composition of
 the recipient population. Here, we experimentally reinforced a house
 sparrow (Passer domesticus) population, and examined the impact of this
 translocation on allele frequencies, levels of heterozygosity and genetic
 differentiation over six cohorts. We found no permanent increase in the
 mean number of alleles across loci or levels of observed heterozygosity,
 but a few alleles private to the translocated individuals remained in the
 population and we found a short-term increase in heterozygosity.
 Consequently, genetic differentiation of the recipient population compared
 to the genetic composition prior to reinforcement was small. The limited
 genetic impact was due to combined effects of a small probability of
 establishment and low mating success for the translocated individuals,
 together with increased genetic drift in the recipient population. Our
 findings emphasize the importance of selection and genetic drift as forces
 that may decrease the genetic contribution of reinforcement, especially in
 small populations. Conservation managers should aim to improve habitat
 quality in the recipient population to reduce genetic drift following
 translocation and thereby avoid the need for continued reinforcement.
 Furthermore, by facilitating establishment success and selecting
 individuals expected to have high mating success, possibly indicated by
 sexually selected traits, genetic contribution of released individuals is
 increased which in turn will decrease reproductive skew and genetic drift.
description: Microsatellite data supporting the study of multi-generational
 genetic consequences of reinforcement in a bird metapopulation. The
 dataset consists of data on 13 microsatellite markers in house sparrow
 individuals following a translocation. Blood samples were collected from
 each individual. The translocated, resident and admixed
 (translocated+resident) groups comprise the starting population, and
 individuals present each year is noted under the group variable.
description: Missing values are depicted with NA. Column
 desciption <strong>ID</strong><br>
 unique identifier
 <strong>Individual_ID</strong><br> individual
 identifier <strong>GROUP</strong><br>
 translocated, resident, admixed, (and whether established or not), then
 six consecutive years. rest of the columns are the 13
 micro satellite markers<br> <strong>Ase18, Pdo1, Pdo10, Pdo16,
 Pdo17, Pdo19, Pdo22, Pdo27, Pdo3, Pdo40, Pdo44, Pdo47,
 Pdo5</strong>
DOI: 10.15468/dl.efkjkd
title: Occurrence Download

description: A dataset containing 123 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Angylocalyx talbotii",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 123 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002312-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.70rxwdbtv
title: Consistent measures of oxidative balance predict survival but not reproduction in a long-distance migrant

description: 1. Physiological processes, including those that disrupt oxidative
 balance, have been proposed as key to understanding fundamental life
 history trade-offs. Yet examination of changes in oxidative balance within
 wild animals across time, space and major life history challenges remain
 uncommon. For example, migration presents substantial physiological
 challenges for individuals, and data on migratory individuals would
 provide crucial context for exposing the importance of relationships
 between oxidative balance and fitness outcomes. 2. Here we examined the
 consistency of commonly used measures of oxidative balance in
 longitudinally sampled free-living individuals of a long-lived,
 long-distance migrant, the Brent goose Branta bernicla hrota over periods
 of months to years. 3. Although inter-individual and temporal variation in
 measures of oxidative balance were substantial, we found high consistency
 in measures of lipid peroxidation and circulating non-enzymatic
 antioxidants in longitudinally sampled individuals. This suggests the
 potential for the existence of individual oxidative phenotypes. 4. Given
 intra-individual consistency, we then examined how these physiological
 measures relate to survival and reproductive success across all sampled
 individuals. Surprisingly, lower survival was predicted for individuals
 with lower levels of damage, with no measured physiological metric
 associated with reproductive success. 5. Our results demonstrate that
 snapshot measurements of a consistent measure of oxidative balance can
 inform our understanding of differences in a key demographic trait.
 However, the positive relationship between oxidative damage and survival
 emphasises the need to investigate relationships between the oxidative
 system and fitness outcomes in other species undergoing similar
 physiologically challenging lifecycles. This would highlight the extent to
 which variation in such traits and resource allocation trade-offs is a
 result of adaptation to different life history strategies. 30-Mar-2020
description: Live capture of wild brent geese using cannon nets on wintering
 and staging grounds. Blood sampling from tarsal vein -
 each sample centrifuged and flash frozen in the field. Samples maintained
 at -80 prior to analysis. Aliquots of plasma assayed
 for malondialdehyde, super oxide dismutase, total antioxidant and uric
 acid concenrations.
description: Many birds do not have all four of the oxidative stress
 assays Birds do not always have a current or subsequent
 associate status (single/pair/family) if this could not be accurately
 assigned in the field
DOI: 10.25338/b8b03q
title: Comparative analysis of pesticide use across California crops

description: Pesticide use is a key component of efficient crop production, but is
 associated with a suite of costs. Understanding the main drivers of
 pesticide use will help us target research to develop effective
 alternatives. Although economic models predict, and empirical tests
 confirm, that the value of the crop being protected is an important
 determinant of between crop variation in pesticide use, previous tests of
 this prediction have examined only modest numbers of crops and have not
 assessed the relative importance of crop value versus ecological
 determinants of pesticide use. Here we analyze variation in pesticide use
 across 93 crops grown in California, USA.We examine the joint roles of
 crop value and ecological determinants of pesticide use, including (i) the
 number of pest species associated with each crop; (ii) the distinction
 between annual vs. perennial crops; and (iii) the distinction between
 unprocessed vs. processed crops. We conclude that both economic and
 ecological drivers influence the magnitude of potential crop losses,
 thereby shaping farmer pest control practices.
description: Data were gathered from public sources, including the California
 Department of Pesticide Regulation's Pesticide Use Reporting
 tool. Other data on crop value and acreage were collected from California
 Department of Food and Agriculture (https://www.cdfa.ca.gov/statistics/).
description: This dataset summarizes mean annual pesticide use in California,
 2011-2015, across 93 crops. Please see the full publication (Rosenheim et
 al.) in Science of the Total Environment for details.
DOI: 10.5281/zenodo.18395199
title: THE SOCIAL AND SUFI CONCEPT IN THE WORKS OF ISMOILXON FAQIRIY

description: This article examines the poetic interpretation of people’s suffering and the artistic representation of the idea of justice in the works of Ismoilkhon Faqiriy from the perspective of a socio-Sufi conception. The study analyzes the close interrelation between social themes and Sufi thought in the poet’s lyrics, focusing on the depiction of social injustice, oppression, poverty, and spiritual decline. It is argued that in Faqiriy’s poetry, people’s pain transcends individual emotion and becomes a generalized social phenomenon. Particular attention is paid to key notions such as faqr (spiritual poverty), patience, contentment, and justice, which the poet enriches with philosophical and mystical meanings and employs as instruments of artistic social critique.
DOI: 10.5281/zenodo.18395200
title: THE SOCIAL AND SUFI CONCEPT IN THE WORKS OF ISMOILXON FAQIRIY

description: This article examines the poetic interpretation of people’s suffering and the artistic representation of the idea of justice in the works of Ismoilkhon Faqiriy from the perspective of a socio-Sufi conception. The study analyzes the close interrelation between social themes and Sufi thought in the poet’s lyrics, focusing on the depiction of social injustice, oppression, poverty, and spiritual decline. It is argued that in Faqiriy’s poetry, people’s pain transcends individual emotion and becomes a generalized social phenomenon. Particular attention is paid to key notions such as faqr (spiritual poverty), patience, contentment, and justice, which the poet enriches with philosophical and mystical meanings and employs as instruments of artistic social critique.