cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.4ha4th
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen, Living Specimen)",
 "Geometry POLYGON((24.353279683971195 45.08833061053375,24.38552832813427 45.08833061053375,24.38552832813427 45.12057925469683,24.353279683971195 45.12057925469683,24.353279683971195 45.08833061053375))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Animalia",
 "Year 1980-2025"
 ]
}

 The dataset includes 60 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011377-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rd3km6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Maulisia mauli Parr, 1960",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((42.8012 -16.5547,42.4342 -16.6376,42.2188 -17.038,42.391 -17.4288,42.6657 -17.5533,43.0375 -17.4752,43.2579 -17.0968,43.0959 -16.69,42.8012 -16.5547))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011379-250525065834625/datasets/export for details.
DOI: 10.15468/dl.h7unr5
title: Occurrence Download

description: A dataset containing 486 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Chamaesyce hyssopifolia (L.) Small",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 486 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011378-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c4r8am
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Maulisia mauli Parr, 1960",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((40.3006 -16.7147,40.6365 -16.1504,35.9648 -16.1504,35.9648 -19.5556,36.0796 -19.4498,36.663 -19.2358,37.5966 -18.1093,38.5624 -17.638,39.3949 -17.5133,39.577 -17.186,40.3006 -16.7147))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011381-250525065834625/datasets/export for details.
DOI: 10.15468/dl.grt7qw
title: Occurrence Download

description: A dataset containing 125 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Chenopodium aristatum L.",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 125 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011382-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8czvb2
title: Occurrence Download

description: A dataset containing 86 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Achillea millefolium L., Achillea ptarmica L., Agrostis canina L., Agrostis capillaris L., Alchemilla monticola Opiz, Anthoxanthum odoratum L., Anthriscus sylvestris (L.) Hoffm., Bubulcus ibis (Linnaeus, 1758), Carex aquatilis Wahlenb., Carex nigra (L.) Reichard, Cerastium fontanum Baumg., Chloephaga picta (J.F.Gmelin, 1789), Columba livia J.F.Gmelin, 1789, Cystopteris fragilis (L.) Bernh., Deschampsia cespitosa (L.) P.Beauv., Avenella flexuosa (L.) Drejer, Elymus repens (L.) Gould, Empetrum rubrum Vahl ex Willd., Equus caballus Linnaeus, 1758, Festuca ovina L., Festuca rubra L., Juncus filiformis L., Lobelia pratiana Gaudich., 1829, Lotus corniculatus L., Mus musculus Linnaeus, 1758, Nardus stricta L., Oryctolagus cuniculus (Linnaeus, 1758), Passer domesticus (Linnaeus, 1758), Poa annua L., Poa pratensis L., Poa trivialis L., Rangifer tarandus tarandus, Ranunculus acris L., Ranunculus repens L., Rattus norvegicus (Berkenhout, 1769), Rumex acetosella L., Sagina procumbens L., Taraxacum campylodes G.E.Haglund, Trifolium repens L., Vaccinium vitis-idaea L.)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Specimen)"
 ]
 }
 },
 "Geometry POLYGON ((-36.2007 -54.24069, -36.27164 -54.15932, -36.29205 -54.14906, -36.43816 -54.10664, -36.60758 -54.11409, -36.74735 -54.17211, -36.80908 -54.25787, -36.78273 -54.35678, -36.69724 -54.42426, -36.63404 -54.44652, -36.45864 -54.46364, -36.29667 -54.4204, -36.2027 -54.33617, -36.2007 -54.24069))"
 ]
}

 The dataset includes 86 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011383-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5r3fc4
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Maulisia mauli Parr, 1960",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((35.9919 -21.4718,35.9648 -21.4413,35.9648 -24.1383,36.0558 -23.8719,35.9919 -21.4718))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011384-250525065834625/datasets/export for details.
DOI: 10.15468/dl.rntrz9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Maulisia mauli Parr, 1960",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((44.9648 10.8496,35.9648 10.8496,35.9648 1.8496,44.9648 1.8496,44.9648 10.8496))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011386-250525065834625/datasets/export for details.
DOI: 10.15468/dl.ny7x6w
title: Occurrence Download

description: A dataset containing 3543 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Chenopodium glaucum L.",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 3543 records from 157 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011385-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zdahqg
title: Occurrence Download

description: A dataset containing 19530 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amaranthus blitoides S.Watson"
 ]
}

 The dataset includes 19530 records from 526 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011387-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gqvrrn
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Maulisia mauli Parr, 1960",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((44.9096 1.1987,44.9648 1.2321,44.9648 1.8496,35.9648 1.8496,35.9648 -7.1504,40.3029 -7.1504,40.4263 -6.8134,40.0733 -6.4249,39.9535 -5.9102,40.3587 -5.2718,40.3515 -4.7573,40.0702 -4.4392,40.3811 -3.7186,40.7402 -3.0348,41.8195 -2.1723,43.8399 0.2902,44.9096 1.1987))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011389-250525065834625/datasets/export for details.
DOI: 10.15468/dl.4qaj9b
title: Occurrence Download

description: A dataset containing 169 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Chenopodium polygonoides (Murr) Aellen",
 "Year is less than or equal to 2000",
 "Year is greater than or equal to 1970",
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 169 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011390-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.brv15dv9q
title: Testing assumptions of nitrogen cycling between a temperate, model coral host and its facultative symbiont: symbiotic contributions to dissolved inorganic nitrogen assimilation

description: Coral symbioses are predicated on the need for mutual nutrient acquisition
 and translocation between partners. Carbon translocation is well-studied
 in this classic mutualism, while nitrogen (N) has received comparatively
 less attention. Quantifying the mechanisms and dynamics of N assimilation
 is critical to understanding the functional ecology of coral organisms.
 Given the importance of symbiosis to the coral holobiont, it is important
 to determine what role photosynthetic symbionts play in N acquisition. We
 used the facultatively symbiotic temperate coral Astrangia poculata and
 15N labeling to test the effects of symbiotic state and trophic status on
 N acquisition. We tracked assimilation of 2 forms of isotopically labeled
 dissolved inorganic N (DIN: ammonium, 15NH4+ and nitrate, 15NO3−) by fed
 and starved colonies of both symbiotic and aposymbiotic A. poculata. Coral
 holobiont tissue was subsequently analyzed for δ15N and changes in
 photosynthetic efficiency. Results suggest that corals acquired the most N
 from DIN via their symbiont Breviolum psygmophilum and that NH4+ is more
 readily assimilated than NO3−. Photosynthetic efficiency increased with
 the addition of NH4+, but only for fed, symbiotic treatments. NO3−
 adversely affected photosynthetic efficiency among starved corals. Our
 results suggest that symbiosis is advantageous for DIN acquisition, that
 dysbiosis inhibits corals’ mixotrophic strategy of nutrient acquisition,
 and that either feeding or symbiosis alone does not fully provide the
 energetic advantage of both. This study lends support to the emerging
 hypothesis that symbionts are mutualists in optimal conditions but shift
 to a parasitic paradigm when resources or energy are scarce.
description: This is an excel file with annotated raw data. Each column
 contains the data collected for a different nutritional variable, protein
 concentration, or photosynthetic efficiency. Each row represents an
 individual colony. Blank cells indicate that data was not collected for
 that colony.
DOI: 10.5061/dryad.v15dv41wg
title: Phylogeography of the sea urchin genus Echinothrix.

description: The sea urchins Echinothrix calamaris and E. diadema have sympatric
 distributions throughout the Indo-Pacific. Diverse colour variation is
 reported in both species. To reconstruct the phylogeny of the genus and
 assess gene flow across the Indo-Pacific we sequenced mitochondrial 16S
 rDNA, ATPase-6, and ATPase-8, and nuclear 28S rDNA and the Calpain-7
 intron. Our analyses revealed that E. diadema formed a single
 trans-Indo-Pacific clade, but E. calamaris contained three discreet
 clades. One clade was endemic to the Red Sea and the Gulf of Oman. A
 second clade occurred from Malaysia in the West to Moorea in the East. A
 third clade of E. calamaris was distributed across the entire Indo-Pacific
 biogeographic region. A fossil calibrated phylogeny revealed that the
 ancestor of E. diadema diverged from the ancestor of E. calamaris ~16.8
 million years ago (Ma), and that the ancestor of the trans-Indo-Pacific
 clade and Red Sea and Gulf of Oman clade split from the western and
 central Pacific clade ~9.8 Ma. Time since divergence and genetic distances
 suggested species level differentiation among clades of E. calamaris.
 Colour variation was extensive in E. calamaris, but not clade or locality
 specific. There was little colour polymorphism in E. diadema.
description: <em>Echinothrix</em> collection data with
 corresponding voucher numbers and GenBank Accession numbers can be found
 in supplementary Table S8 (a link will be provided when the data are
 published)
DOI: 10.5061/dryad.jm63xsjbh
title: Data from: Using local ecological knowledge to build mutualistic networks in hyper-diverse and logistically challenging ecosystems

description: 1. Collecting interaction data to build frugivory or seed
 dispersal networks is logistically challenging in ecosystems that have
 very high plant and animal diversity and/or where fieldwork is difficult
 or dangerous. Consequently, the majority of available networks are from
 ecosystems with low species diversity or they represent a sub-set of the
 community.  2. Here, we propose an approach using local
 ecological knowledge (LEK) of indigenous communities to build interaction
 databases and weighted networks that would otherwise be difficult to
 achieve with direct observations. Indigenous communities live and work in
 many hyper-diverse ecosystems and the people within these communities
 often have detailed knowledge of ecological processes. 
 3. Working in a Sundaland biodiversity hotspot – Royal Belum
 State Park, Peninsular Malaysia – we used field data, visually-oriented
 interviews with indigenous people (Orang Asli, in the Jahai and Temiar
 ethnic subgroups), and published records to collate interactions, and
 their frequency of occurrence of animal fruit consumption and seed
 dispersal.  4. We documented 2060 fruit consumption and
 1330 seed dispersal interactions among 164 plant species and 34 animal
 taxa, the latter representing groups of closely related species or
 individual species. The majority of the interactions (97%) were identified
 by the LEK interviews, with the additional methods (field data and
 published records) used to support and marginally expand the interview
 data. The metrics for the networks we built reflect those of networks
 structured by biological mechanisms, supporting the validity of our novel
 method.  5. Local ecological knowledge is highly
 relevant for building detailed databases for mutualistic interactions in
 hyper-diverse and/or challenging ecosystems. Such ecosystems are among the
 most vulnerable on earth, harbouring ecological interactions that are
 often poorly documented at a community-level. We show how LEK can broaden
 our knowledge of such sensitive ecosystems, but our approach is useful for
 any ecosystem where people retain rich local ecological knowledge.
description: The method is fully described in Ong et al. (2021),
 "Building ecological networks with local ecological knowledge in
 hyper-diverse and logistically challenging ecosystems". Further
 details are provided in the online supplementary materials.
description: This dataset contains frugivory and seed dispersal interactions
 collected largely based on local ecological knowledge provided by the
 indigenous people of the Belum rainforest in Peninsular Malaysia, Sundaic
 region. It includes fruit consumption and seed dispersal matrices tested
 in Ong et al. (2021).
DOI: 10.5061/dryad.sn02v6x4g
title: Classification of the UBCF_13 COG based on COG database in NCBI

description: Background: The Serratia plymuthica UBCF_13 is a phylloplane associated
 plant bacterium showing antifungal activity. Whole genome sequence
 provides information to get more insight about evolutionary study, unique
 traits in the genome and possibility to explore potential of this
 microorganism for future study. Here, we report the genome sequence of S.
 plymuthica UBCF_13 and the comparison with other seventeen strain.
 Methods: Continuous short reads were attained from Illumina sequencing
 runs and reads of 150 bp were merged into a single dataset. A pan-genome
 based method was used to identify the core-genome of S. plymuthica species
 and the unique gene in UBCF-13. Results: Assembled Illumina reads of S.
 plymuthica strain UBCF_13 genome was produced a 5.46 Mb circular genome
 sequence. 3315 genes were found to belong to the core-genome sheared by
 the 18 strains evaluated. The UBCF_13 genome harbors 488 unique genes,
 where 300 of which only can be found in this strain. The raw and assembled
 data is available via NCBI Short Read Archive (accession Number:
 SRR15012717) and genome database (accession number: CP068771).
description: Translated
 protein coding genes of UBCF_13 was used to identification of cluster of
 orthologous groups (COG). It was obtained by NCBI BLAST+rpsblast (Galaxy
 Version 2.10.1+galaxy0) and eggNOG Mapper (Galaxy Version 2.0.1+galaxy1)
 (eggNOG, RRID:SCR_002456). The result of COG assignment was classified
 based on categories in COG database NCBI.
DOI: 10.5061/dryad.gf1vhhmqd
title: The novel concept of diversity at giving-up density (DivGUD) in experimental ressource landscapes of 9 food patches explored by Norway rats

description: Foraging by consumers acts as a biotic filtering mechanism for
 biodiversity at the trophic level of resources. Variation in foraging
 behaviour have cascading effects on abundance, diversity, and functional
 trait composition of the community of resource species. Here we propose
 diversity at giving-up density (DivGUD), when foragers quit exploring a
 patch, as a novel concept and simple measure to quantify these effects at
 multiple spatial scales. In experimental landscapes, patch residency of
 wild rodents decreased local α-DivGUD (via elevated mortality of species
 with large seeds) and regional γ-DivGUD, while dissimilarity among patches
 in a landscape (ß-DivGUD) increased. Thus, DivGUD provides a framework
 linking theories of adaptive foraging behaviour with community ecology
 allowing to investigate cascading indirect predation effects across
 multiple trophic levels e.g. the ecology-of-fear framework; feedbacks
 between functional trait composition of resource species and consumer
 communities; and effects of inter-individual differences among foragers on
 the biodiversity of resource communities.
description: We created resource landscapes with nine experimental food
 patches, 10 m apart from each other in a 30 x 30 m grid (deployment). Each
 patch contained a 30 cm x 30 cm x 3 cm seed tray with 2 litres fine
 grained sand (0.1-0.5 mm grain size) and a mix of seeds from 8 different
 plant species, varying in functional traits of seeds (Table 2) such as
 size, mass, nutritional value, or presence of husks (initial density of 20
 seed items of 8 seed species per patch). Trays were equipped with a camera
 trap to identify foraging animals and covered with Perspex corrugated
 plastic as rain protection. After exposure of food patches to foragers
 overnight, we sifted the remaining seeds from the sand and counted them by
 species to obtain seed-specific giving-up density (GUD, items per liter of
 sand). Data represents seed counts from food patches after exploitation by
 wild Norway rats that extracted seeds from the sand. PatchID reports
 replicate (R3-R9, chronologically, missing numbers indicate replicates
 without foraging events), grid ID (E4 or E5), and tray location (T1-T9);
 residency (minutes a rat spent in pach) were observed with camera traps
 (in two occasions (*) cameras were foggy during parts of night and
 residency was extrapolated from unspecific, cumulative GUD), followed by
 item counts of the 8 seed species.
description: Missing numbers in patch ID indicate replicates without foraging
 events, i.e. replicates where no seeds were taken and the initial density
 of 20 seed items of 8 seed species remained.
DOI: 10.5061/dryad.wh70rxwnr
title: Cambrian comb jellies from Utah illuminate the early evolution of nervous and sensory systems in ctenophores - Phylogenetic dataset

description: Ctenophores are a group of predatory macroinvertebrates whose
 controversial phylogenetic position has prompted several competing
 hypotheses regarding the evolution of animal organ systems. Although
 ctenophores date back at least to the Cambrian, they have a poor fossil
 record due to their gelatinous bodies. Here, we describe two ctenophore
 species from the Cambrian of Utah, which illuminate the early evolution of
 nervous and sensory features in the phylum. Thalassostaphylos elegans has
 16 comb rows, an oral skirt, and an apical organ with polar fields.
 Ctenorhabdotus campanelliformis has 24 comb rows, an oral skirt, an apical
 organ enclosed by a capsule and neurological tissues preserved as
 carbonaceous films. These are concentrated around the apical organ and
 ciliated furrows, which connect to a circumoral nerve ring via
 longitudinal axons. C. campanelliformis deviates from the neuroanatomy of
 living ctenophores, and demonstrates a substantial complexity in the
 nervous system of Cambrian ctenophores.