cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.31065886
title: <b>A Genome-Resolved Metagenomic Atlas of Pacific Deep-Sea Polymetallic Nodules and Associated Sediments</b>

description: This Data Descriptor presents a genome-resolved metagenomic dataset from deep-sea sediments and polymetallic nodules collected across multiple Pacific Ocean. The dataset integrates 22 newly generated metagenomes with 24 publicly available datasets, comprising sediment cores spanning vertical depth profiles and polymetallic nodule samples collected at abyssal water depths. Metagenomic assembly and gene prediction produced over 147 million protein-coding sequences, which were clustered into a non-redundant gene catalog of more than 65 million representative genes with multi-database functional and taxonomic annotations. Genome binning and dereplication yielded 1,680 species-level metagenome-assembled genomes spanning diverse bacterial and archaeal lineages. Together, the non-redundant gene catalog and MAG collection provide a reference resource for comparative genomics, functional annotation, and ecological analyses of microbial communities associated with deep-sea nodule-bearing environments, and support future studies on microbial diversity, metabolic potential, and environmental assessments in abyssal ecosystems.<br>
DOI: 10.6084/m9.figshare.31065886.v1
title: <b>A Genome-Resolved Metagenomic Atlas of Pacific Deep-Sea Polymetallic Nodules and Associated Sediments</b>

description: This Data Descriptor presents a genome-resolved metagenomic dataset from deep-sea sediments and polymetallic nodules collected across multiple Pacific Ocean. The dataset integrates 22 newly generated metagenomes with 24 publicly available datasets, comprising sediment cores spanning vertical depth profiles and polymetallic nodule samples collected at abyssal water depths. Metagenomic assembly and gene prediction produced over 147 million protein-coding sequences, which were clustered into a non-redundant gene catalog of more than 65 million representative genes with multi-database functional and taxonomic annotations. Genome binning and dereplication yielded 1,680 species-level metagenome-assembled genomes spanning diverse bacterial and archaeal lineages. Together, the non-redundant gene catalog and MAG collection provide a reference resource for comparative genomics, functional annotation, and ecological analyses of microbial communities associated with deep-sea nodule-bearing environments, and support future studies on microbial diversity, metabolic potential, and environmental assessments in abyssal ecosystems.<br>
DOI: 10.5061/dryad.7dg0p
title: Data from: Speciation is not necessarily easier in species with sexually monomorphic mating signals

description: Should we have different expectations regarding the likelihood and pace of
 speciation by sexual selection when considering species with sexually
 monomorphic mating signals? Two conditions that can facilitate rapid
 species divergence are Felsenstein's one-allele mechanism and a
 genetic architecture that includes a genetic association between signal
 and preference loci. In sexually monomorphic species, the former can
 manifest in the form of mate choice based on phenotype matching. The
 latter can be promoted by selection acting upon genetic loci for divergent
 signals and preferences expressed simultaneously in each individual rather
 than separately, on signal loci in males and preference loci in females.
 Both sexes in the Chrysoperla carnea-group of green lacewings (Insecta,
 Neuroptera, Chrysopidae) produce sexually monomorphic species-specific
 mating signals. We hybridized the two species C. agilis and C. carnea to
 test for evidence of these speciation-facilitating conditions. Hybrid
 signals were more complex than the parents and we observed a dominant
 influence of C. carnea. We found a dominant influence of C. agilis on
 preferences in the form of hybrid discrimination against C. carnea.
 Preferences in hybrids followed patterns predicting preference loci that
 determine mate choice rather than a one-allele mechanism. The genetic
 association between signal and preference we detected in the segregating
 hybrid crosses indicate that speciation in these species with sexually
 monomorphic mating signals can have occurred rapidly. However, we need
 additional evidence to determine whether such genetic associations form
 more readily in sexually monomorphic species compared to dimorphic species
 and consequently facilitate speciation.
description: Raw and processed mating
 signal data, and processed preference dataData used for tests of
 signal inheritance and correlation between signal and
 preference.achybrid_signal_and_preference.txtPlayback signals measured for temporal signal featuresPlayback signals used in experiment, measured for temporal signal features. Column 2 corresponds to the most preferred playback signal based on bayespref individual model prediction in Column 18 of file: achybrid_signal_and_preference.txtplayback_signals_measured.txtRaw preference dataData used to estimate mate preferences. Archive consists of 6 files that contain the raw counts of responses that individuals made to each playback signal, and includes files for the experimental and preliminary (lab) populations.raw_preference_counts.tar.gz
DOI: 10.5061/dryad.8q7h4g7
title: Data from: Ontogenetic resource utilization and migration reconstruction with δ13C values of essential amino acids in the Cynoscion acoupa otolith

description: 1. With the increasing anthropogenic impacts on fish habitats, it has
 become more important to understand which primary resources sustain fish
 populations. This resource utilization can differ between fish life stages
 and individuals can migrate between habitats in search of resources. Such
 lifetime information is difficult to obtain due to the large spatial and
 temporal scales of fish behaviour. The otolith organic matrix has the
 potential to indicate this resource utilization and migration with δ13C
 values of essential amino acids (EAAs), which are a direct indication of
 the primary producers. 2. In a proof-of-concept study, we selected the
 Acoupa weakfish, Cynoscion acoupa, as a model fish species with distinct
 ontogenetic migration patterns. While it inhabits the Brazilian mangrove
 estuaries during juvenile stages, it moves to the coastal shelf as an
 adult. Thus, we expected that lifetime resource utilization and migration
 would be reflected in δ13CEAA patterns and baseline values in C. acoupa
 otoliths. 3. By analysing the C. acoupa otolith edges across a size range
 of 12 to 119 cm, we found that baseline δ13CEAA values increased with
 size, which indicated an estuarine to coastal shelf distribution. This
 trend is highly correlated with inorganic δ13C values. The δ13CEAA
 patterns showed that estuarine algae rather than mangrove-derived
 resources supported the juvenile C. acoupa populations. Around the
 juvenile size of 40 cm, resource utilization overlapped with those of
 adults and mean baseline δ13CEAA values increased. This trend was
 confirmed by comparing otolith core and edges, although with some
 individuals potentially migrating over longer distances than others. 4.
 Hence, δ13CEAA patterns and baseline values in otoliths have great
 potential to reconstruct ontogenetic shifts in resource use and habitats.
 The insight could aid in predictions on how environmental changes affect
 fish populations by identifying the controlling factors at the base of the
 food web.
description: d13C values of essential
 amino acids in C. acoupa otolithsData_deposit.xlsx
DOI: 10.5061/dryad.7sj32
title: Data from: Villages and their old farmsteads are hot spots of bird diversity in agricultural landscapes

description: To counteract the decline of farmland biodiversity in Europe, it is
 crucial to recognize habitats that are hot spots. Old rural settlements
 (e.g. villages) may be such important habitats, although these presumably
 biodiversity-rich habitats have received little attention. Socio-economic
 changes in central-eastern Europe since 1989 mean that old homesteads and
 farmsteads are being replaced by new ones. We investigated bird species
 composition, richness and abundance at three spatial scales (single rural
 property, village and landscape) in the farmland of Poland to test: (i)
 their association with age (built before vs. after 1989) and type of
 property (farmstead vs. homestead), (ii) their relationship with the
 increasing share of new homesteads at the village scale and (iii) the
 difference in diversity between the village environment and four other
 environments (open fields, forest–field ecotones, forests and towns) at
 the landscape scale. At the single property scale, 15 out of 33 species
 preferred old farmsteads, while only one species preferred new homesteads.
 Old properties hosted a higher number of species and individuals than new
 ones, and farmsteads hosted a higher number of species than homesteads. At
 the village scale, bird species richness and abundance were markedly
 negatively associated with the proportion of new homesteads. At the
 landscape scale, species composition differed between villages and the
 other environments, and villages had the highest average bird abundance.
 Synthesis and applications. Rural villages and old farmsteads are
 important habitats for many farmland birds; thus, the increasing number of
 new homesteads not associated with farmland production will likely lead to
 a substantial further decline of farmland bird numbers and biodiversity.
 To counteract this process, we recommend (i) implementing educational
 programmes to develop rural residents’ awareness about the importance of
 farmsteads and homesteads for biodiversity, (ii) including villages and
 farmsteads and consideration of bird-friendly habitats within these as
 part of EU conservation policies and (iii) compensating for changes in the
 structure of rural villages by increasing the amount of similar
 alternative habitats in the surrounding landscape.
description: data_property_scaledata_village_scaledata_landscape_scale
DOI: 10.15468/dl.mz9r77
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Withania begoniifolia",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 12 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001025-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5b6f7
title: Data from: Links between parental life histories of wild salmon and the telomere lengths of their offspring

description: The importance of parental contributions to offspring development and
 subsequent performance is self-evident at a genomic level; however,
 parents can also affect offspring fitness by indirect genetic and
 environmental routes. The life history strategy that an individual adopts
 will be influenced by both genes and environment; and this may have
 important consequences for offspring. Recent research has linked telomere
 dynamics (i.e. telomere length and loss) in early life to future viability
 and longevity. Moreover, a number of studies have reported a heritable
 component to telomere length across a range of vertebrates, though the
 effects of other parental contribution pathways have been far less
 studied. By using wild Atlantic salmon with different parental life
 histories in an experimental split-brood IVF mating design and rearing the
 resulting families under standardised conditions, we show that there can
 be significant links between parental life history and offspring telomere
 length (studied at the embryo and fry stage). Maternal life history
 traits, in particular egg size, were most strongly related to offspring
 telomere length at the embryonic stage, but then became weaker through
 development. In contrast, paternal life history traits, such as the
 father’s growth rate in early life, had a greater association in the later
 stages of offspring development. However, offspring telomere length was
 not significantly related to either maternal or paternal age at
 reproduction, nor to paternal sperm telomere length. This study
 demonstrates both the complexity and the importance of parental factors
 that can influence telomere length in early life.
description: Embryo relative telomere
 lengthData contained in this
 spread sheet relates to the linear mixed model assessing variation in
 embryo relative telomere length.Variation in embryo
 RTL.xlsxFry relative telomere
 lengthData contained in this
 spread sheet relates to the linear mixed model assessing variation in fry
 relative telomere length.Variation in fry
 RTL.xlsxParental relative
 telomere lengthData contained in this
 spread sheet relates to the general linear model assessing variation in
 parental relative telomere length.Variation in parental
 RTL.xlsxSperm relative telomere
 lengthData contained in this
 spread sheet relates to the general linear model assessing variation in
 sperm relative telomere length.Variation in sperm
 RTL.xlsx
DOI: 10.5061/dryad.9011
title: Data from: Molecular profiling of diatom assemblages in tropical lake sediments using taxon-specific PCR and Denaturing High-Performance Liquid Chromatography (PCR-DHPLC)

description: Here we present a protocol to genetically detect diatoms in sediments of
 the Kenyan tropical Lake Naivasha, based on taxon-specific PCR
 amplification of short fragments (approx. 100 bp) of the small subunit
 ribosomal (SSU) gene and subsequent separation of species-specific PCR
 products by PCR-based DHPLC. An evaluation of amplicons differing in
 primer specificity to diatoms and length of the fragments amplified
 demonstrated that the number of different diatom sequence types detected
 after cloning of the PCR products critically depended on the specificity
 of the primers to diatoms and the length of the amplified fragments
 whereby shorter fragments yielded more species of diatoms. The DHPLC was
 able to discriminate between very short amplicons based on the sequence
 difference, even if the fragments were of identical length. and if the
 amplicons differed only in a small number of nucleotides. Generally the
 method identified the dominant sequence types from mixed amplifications. A
 comparison with microscopic analysis of the sediment samples revealed that
 the sequence types identified in the molecular assessment corresponded
 well with the most dominant species. In summary, the PCR-based DHPLC
 protocol offers a fast, reliable, and cost-efficient possibility to study
 DNA from sediments and other environmental samples with unknown organismic
 content, even for very short DNA fragments.
description: Results_Cloning_DHPLC_GenbankAccThis table includes results from cloning and direct sequencing after DHPLC collection, along with the Genbank accession numbers of the retrieved sequences. Reference is made to Figure 3 in the paper.
DOI: 10.15468/dl.rchsc4
title: Occurrence Download

description: A dataset listing the 1588 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-3.15345 38.13147,-3.19325 38.06066,-2.91685 38.0432,-2.90474 38.09224,-2.91685 38.13988,-2.96703 38.16982,-3.11439 38.15208,-3.15345 38.13147))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 1588 records were derived from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001013-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.qm3gb
title: Data from: Shock and stabilisation following long-term drought in tropical forest from 15 years of litterfall dynamics

description: Litterfall dynamics in tropical forests are a good indicator of overall
 tropical forest function, indicative of carbon invested in both
 photosynthesising tissues and reproductive organs such as flowers and
 fruits. These dynamics are sensitive to changes in climate, such as
 drought, but little is known about the long-term responses of tropical
 forest litterfall dynamics to extended drought stress. We present a
 15-year dataset of litterfall (leaf, flower and fruit, and twigs) from the
 world's only long-running drought experiment in tropical forest. This
 dataset comprises one of the longest published litterfall time series in
 natural forest, which allows the long-term effects of drought on forest
 reproduction and canopy investment to be explored. Over the first 4 years
 of the experiment, the experimental soil moisture deficit created only a
 small decline in total litterfall and leaf fall (12% and 13%,
 respectively), but a very strong initial decline in reproductive
 litterfall (flowers and fruits) of 54%. This loss of flowering and
 fruiting was accompanied by a de-coupling of all litterfall patterns from
 seasonal climate variables. However, following &gt;10 years of the
 experimental drought, flower and fruiting re-stabilised at levels greater
 than in the control plot, despite high tree mortality in the drought plot.
 Litterfall relationships with atmospheric drivers were re-established
 alongside a strong new apparent trade-off between litterfall and tree
 growth. Synthesis. We demonstrate that this tropical forest went through
 an initial shock response during the first 4 years of intense drought,
 where reproductive effort was arrested and seasonal litterfall patterns
 were lost. However, following &gt;10 years of experimental drought,
 this system appears to be re-stabilising at a new functional state where
 reproduction is substantially elevated on a per tree basis; and there is a
 new strong trade-off between investment in canopy production and wood
 production.
description: Caxiuana Monthly
 litterfall values 2001-2016Average monthly litter
 fall values for leaves, twigs, flowers and fruits and totals with a
 standard error for the Control and TFE plot at the Caxiuana National
 Reserve Brazil. The data is available for the period of 2001 to
 2016JoE_DRYAD_Caxiuana_Litterfall.xlsx
DOI: 10.5061/dryad.t6b85
title: Data from: The effect of kleptoparasite and host numbers on the risk of food-stealing in an avian assemblage

description: Kleptoparasitism involves the theft of resources such as food items from
 one individual by another. Such food-stealing behaviour can have important
 consequences for birds, in terms of individual fitness and population
 sizes. In order to understand avian host–kleptoparasite interactions,
 studies are needed which identify the factors which modulate the risk of
 kleptoparasitism. In temperate European intertidal areas, Eurasian
 oystercatchers Haematopus ostralegus feed primarily on bivalve molluscs,
 which may be stolen by kleptoparasitic species such as carrion crows
 Corvus corone and herring gulls Larus argentatus. In this study we
 combined overwinter foraging observations of oystercatchers and their
 kleptoparasites on the Exe Estuary, UK, with statistical modelling to
 identify the factors that influence the likelihood of successful food
 stealing behaviour occurring. Across the winter, 16.4% of oystercatcher
 foraging attempts ended in successful kleptoparasitism; the risk of theft
 was lowest in February (10.8%) and highest in December (36.3%). Using an
 information theoretic approach to compare multiple logistic regression
 models we present evidence that the outcome of host foraging attempts
 varied with the number of kleptoparasites per host within the foraging
 patch for two out of five individual months, and for all months grouped.
 Successful, kleptoparasitism was more likely to occur when the total
 number of all kleptoparasites per host was greater. Across the entire
 winter study period, oystercatcher foraging attempts that resulted in
 kleptoparasitism were associated with a mean number of kleptoparasites per
 host that was more than double that for foraging attempts that ended in
 the oystercatcher successfully consuming the mussel. Conversely, the stage
 of the tidal cycle within the estuary did not affect the outcome of
 oystercatcher foraging attempts. Our study provides evidence that bird
 numbers influence the risk of kleptoparasitism within avian assemblages.
description: Data from: The effect of
 kleptoparasite and host numbers on the risk of food-stealing in an avian
 assemblageA .csv file containing
 two spreadsheets. The first ("kleptoparasite pressure") presents
 the binary outcome of oystercatcher foraging attempts in column M, along
 with 12 different measures of kleptoparasite pressure. The second sheet
 ("factors affect kleptoparasitism") presents the binary outcome
 of oystercatcher foraging attempts in column A, along with the following
 data associated with each individual-level observation: month, mussel bed,
 percentage of the tidal cycle elapsed, and the number of kleptoparasites
 per host. Further details on the collection of these data are given in the
 associated published paper in Journal of Avian Biology by Wood et
 al.Wood et
 al 2015 J Avian Biol data.csv