cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2v6wwpzhd
title: Data from: Seed germination schedule and environmental context shaped the population genetic structure of subtropical evergreen oaks on the Yun-Gui Plateau, Southwest China

description: The evergreen broadleaved forests (EBLFs) of Southwest China have a
 long-term stable environment and support a diverse flora, thus forming a
 global biodiversity hotspot. However, the key drivers that have shaped the
 genetic diversity patterns of species in these EBLFs are not well
 understood. Quercus delavayi, Q. schottkyana, and Q. kerrii are sympatric
 oak species with different seed biological traits that are typical for
 these EBLFs. This study combined multilocus phylogeography and ecological
 niche modeling to screen 33 Q. delavayi populations. Their population
 genetic structure was inferred in comparison with previous studies on Q.
 schottkyana and Q. kerrii. The seed germination traits of all three
 species were also investigated. cpDNAs showed a significant
 phylogeographic structure in Q. delavayi, which was not detected in Q.
 schottkyana or Q. kerrii. Quercus delavayi, Q. kerrii, and Q. schottkyana
 exhibited different pollen-to-seed migration ratios (r = 219, 117, and 22,
 respectively), which are linked to the germination schedules of acorns.
 The distributions of Q. delavayi and Q. schottkyana remained long-term
 stable since the last glacial maximum (LGM) with a similar nSSR genetic
 gradient change along latitude. Instead, Q. kerrii experienced a prominent
 range expansion since the LGM with genetic diversification between the
 East and the West of the Tanaka line due to environmental heterogeneity.
 These results identify seed traits and environmental heterogeneity as two
 key drivers that shape the population genetic structure of EBLF trees in
 Southwest China. These should be considered in regional forestry
 conservation and management.
description: SSR data for Quercus delavayi
DOI: 10.5061/dryad.cvdncjt0b
title: Data from: Genotype-by-environment interactions for seminal fluid expression and sperm competitive ability

description: Sperm competition commonly occurs whenever females mate multiply, leading
 to variation in male paternity success. This can be due to variation in
 the various traits that might affect sperm competitive ability, which
 itself depends on both genetic and environmental factors, as well as on
 genotype-by-environment interactions (GEI). Seminal fluid is a major
 component of the male ejaculate that is often expected to mediate sperm
 competition, where different genotypes can differ in their seminal fluid
 expression as a response to different level of sperm competition (i.e.,
 exhibit GEI). We therefore here focussed on testing for GEI in expression
 of two recently identified seminal fluid transcripts, suckless-1 and
 suckless-2, which potentially modulate sperm competitive ability in the
 simultaneously hermaphroditic flatworm Macrostomum lignano via their
 effects on manipulating post-mating partner behaviour and ultimately the
 fate of transferred ejaculates. In addition, we sought to test for GEI in
 sperm competitive ability in a standardised sperm competition (P1
 & P2) assay, to investigate the relationship between natural
 variation in the expression of these seminal fluid transcripts generated
 through GEI and relative paternity success. We found GEI for the
 expression level of suckless-1 and suckless-2, as well as for sperm
 competitive ability. Moreover, we found a positive relation between the
 expression of suckless-1 and relative paternity success (P1). This
 suggests that natural variation in the expression of this seminal fluid
 transcript indeed can influence sperm competition outcomes in M. lignano.
DOI: 10.5061/dryad.0gb5mkkx1
title: Data and code for a high-resolution summary of Cambrian to Early Triassic marine invertebrate biodiversity

description: Data compilation and standardization were conducted through the
 Geobiodiversity Database from 2013 to 2017. The raw dataset contained
 266,110 local Cambrian to Triassic records of 45,318 taxonomic units from
 3,766 published stratigraphic sections. These were collected from all
 major Chinese tectonic plates. The authors spent three years verifying the
 taxonomic assignments into a consistent paleontological taxonomic
 classification system. Identifications to genus or higher taxonomic ranks
 were omitted. All non-marine fossil groups (e.g., plants, vertebrates,
 pollen, spores) were also removed. Species recovered from only a single
 locality were removed after a few test calculations in order to partially
 standardize the sampling and research efforts and avoid the
 "monograph effect". The final dataset retained after all
 standardization procedures included 116,060 local records of the
 stratigraphic ranges of 11,268 species in 3,112 published stratigraphic
 sections.  The CONOP.SAGA program was designed for
 high-performance computing of geological time scale and biodiversity
 analysis in 2017. We designed a special hybrid algorithm that combined
 simulated annealing and a genetic algorithm to overcome the limitations of
 classic CONOP program designed by Pete Sadler.
DOI: 10.5061/dryad.4f4qrfj7h
title: Conflicting signal in transcriptomic markers leads to a poorly resolved backbone phylogeny of Chalcidoid wasps

description: Chalcidoidea (Hymenoptera) are a megadiverse superfamily of wasps with
 astounding variation in both morphology and biology. Most species are
 parasitoids and important natural enemies of insects in terrestrial
 ecosystems. In this study, we explored a transcriptome-based phylogeny of
 Chalcidoidea and found that poorly resolved relationships could only be
 marginally improved by adding more genes (a total of 5,591) and taxa (a
 total of 65), proof-checking for errors of homology and contamination, and
 decreasing missing data. Concatenation analyses consistently place
 Mymaridae and Trichogrammatidae sister to remaining Chalcidoidea. However,
 our coalescent analyses provide a different hypothesis with a grouping of
 (Mymaridae (((Trichogrammatidae, Eulophidae), (Encyrtidae, Aphelinidae)),
 remaining Chalcidoidea)). This hypothesis complicates our hypothesis of
 egg parasitism as being ancestral in Chalcidoidea. At the deeper nodes,
 the results uncovered a wide spectrum of gene discordance in the
 transcriptomic markers and identified a strong signal of functional bias
 in genes supporting alternative phylogenies. The basal nodes of the
 phylogeny are thus strongly influenced by biased support from different
 functional gene complexes. Shallower nodes showed similar gene
 discordance, but without strong functional bias. Understanding and
 identifying mechanisms that result in gene tree discordance may be
 beneficial and even essential for sorting out backbone relationships,
 especially for groups that have undergone extremely rapid radiation.
DOI: 10.15468/dl.9thwr2
title: Occurrence Download

description: A dataset containing 100 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-77.90138 -1.06217,-77.94969 -1.07611,-77.95119 -1.11349,-77.93217 -1.09971,-77.89424 -1.09108,-77.88335 -1.07456,-77.90138 -1.06217))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Amphibia"
 ]
}

 The dataset includes 100 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002030-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xrfgy8
title: Occurrence Download

description: A dataset containing 2254 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Mexico, United States of America)",
 "TaxonKey is Canis lupus baileyi"
 ]
}

 The dataset includes 2254 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002029-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fwktkt
title: Occurrence Download

description: A dataset containing 627 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lestidiops affinis",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 627 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002032-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25934/pr00012546.0
title: Available datapackage for study 'Portable GC Detector for COVID Diagnostics'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.5061/dryad.ncjsxksqt
title: Data from: Ecological transitions in grouping benefits explain the paradox of environmental quality and sociality

description: Both benign and harsh environments promote the evolution of sociality.
 This paradox—societies occur in environments of such contrasting
 quality—may be explained by the different types of benefits that
 individuals receive from grouping: resource defense benefits that derive
 from group-defended critical resources versus collective action benefits
 that result from social cooperation among group member. Here, we
 investigate cooperative behavior in the burying beetle Nicrophorus
 nepalensis along an elevational gradient where environmental quality
 (climate and competiton) varies with altitude. We show that climate
 (temperature) and competition (both intra- and interspecific)
 independently and synergistically influence sociality via different
 grouping benefits that vary along the gradient. At low elevations where
 interspecific competition for resources is intense, groups gain from the
 collective action benefit of increased interspecific competitive ability.
 In contrast, pairs have higher fitness at intermediate elevations where
 intraspecific competition for resources is greatest because resource
 defense is the key grouping benefit. However, groups and pairs have
 similar fitness at high elevations, suggesting that there is no grouping
 benefit in such physiologically challenging environments. Our results
 demonstrate that sociality is favored for different reasons under a range
 of environmental conditions, perhaps explaining why animal societies occur
 in environments of such contrasting quality.
DOI: 10.15468/dl.cauv6p
title: Occurrence Download

description: A dataset containing 585 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Ghana",
 "DatasetKey is one of (EOD – eBird Observation Dataset, Observation.org, Nature data from around the World, iNaturalist Research-grade Observations, NABU|naturgucker, Birda - Global Observation Dataset)",
 "GadmGid is GHA",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is one of (January, February, March, April, May, June, July, August, September, October, November, December)",
 "OccurrenceStatus is Present",
 "TaxonKey is Bucorvus abyssinicus",
 "Year 1980-2026"
 ]
}

 The dataset includes 585 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002033-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.j6q573n8j
title: Fidelity to foraging sites after long migrations

description: 1. Patterns of animal movement associated with foraging lie at the heart
 of many ecological studies and often animals face decisions of staying in
 an environment they know, versus relocating to new sites. 2. The lack of
 knowledge of new foraging sites means there is risk associated with a
 decision to relocate (e.g. poor foraging) as well as a potential benefit
 (e.g. improved foraging). 3. Using a unique long-term satellite tracking
 dataset for several sea turtle species, combined with
 capture-mark-recapture (CMR) data extending over 50 years, we show how,
 across species, individuals generally maintain tight fidelity to specific
 foraging sites after extended (up to almost 10,000 km) migration to and
 from distant breeding sites as well as across many decades. 4. Migrating
 individuals often travelled through suitable foraging areas en route to
 their “home” site and so extended their journeys to maintain foraging site
 fidelity. 5. We explore the likely mechanistic underpinnings of this
 trait, which is also seen in some migrating birds, and suggest that
 individuals will forgo areas of suitable forage encountered en route
 during migration when they have poor knowledge of the long-term
 suitability of those sites, making relocation to those sites risky.
DOI: 10.5061/dryad.cz8w9gj03
title: Generalised host-plant feeding can hide sterol specialised foraging behaviours in bee-plant interactions

description: Host-plant selection is a key factor driving the ecology and evolution of
 insects. While the majority of phytophagous insects are highly host
 specific, generalist behaviour is quite widespread among bees and
 presumably involves physiological adaptations that remain largely
 unexplored. However floral visitation patterns suggest that generalist
 bees do not forage randomly on all available resources. While resource
 availability and accessibility as well as nectar composition have been
 widely explored, pollen chemistry could also have an impact on the range
 of suitable host-plants. This study focuses on particular pollen nutrients
 that cannot be synthesised de novo by insects but are key compounds of
 cell membranes and the precursor for moulting process: the sterols. We
 compared the sterol composition of pollen from the main host-plants of
 three generalist bees: Anthophora plumipes,Colletes
 cuniculariusand Osmia cornuta, as well as one specialist
 bee Andrena vaga. We also analysed the sterols of their brood
 cell provisions, the tissues of larvae and non-emerged females to
 determine which sterols are used by the different species. Our results
 show that sterols are not used accordingly to foraging strategy: Both the
 specialist species Andrena vagaand the generalist
 species Colletes cuniculariusmight metabolise a rare C27sterol,
 while the two generalist species Anthophora
 plumipesand Osmiacornutamight rather use a very common C28sterol.
 Our results suggest that shared sterolic compounds among plant species
 could facilitate the exploitation of multiple host-plants by A.
 plumipesand O. cornutawhereas the generalist C.
 cuniculariusmight be more constrained due to its physiological
 requirements of a more uncommon dietary sterol. Our findings suggest that
 a bee displaying a generalist foraging behaviour may sometimes hide a
 sterol-specialised species. This evidence challenges the hypothesis that
 all generalist free-living bee species are all able to develop on a wide
 range of different pollen types.
DOI: 10.5061/dryad.sqv9s4n0g
title: Maternal diet affects juvenile Carpetan rock lizard performance and personality

description: Differences in both stable and labile state variables are known to affect
 the emergence and maintenance of consistent inter-individual behavioural
 variation (animal personality or behavioural syndrome), especially when
 experienced early in life. Variation in environmental conditions
 experienced by gestating mothers (viz. non-genetic maternal effects) are
 known to have significant impact on offspring condition and behaviour,
 yet, their effect on behavioural consistency is not clear. Here, by
 applying an orthogonal experimental design, we aimed to study if increased
 vitamin D3 content in maternal diet during gestation (vitamin-supplemented
 vs. vitamin control treatments) combined with corticosterone treatment
 (corticosterone-treated vs. corticosterone control treatments) applied on
 freshly hatched juveniles had an effect on individual state and
 behavioural consistency of juvenile Carpetan rock lizards (Iberolacerta
 cyreni). We tested the effect of our treatments on (i) climbing speed and
 the following levels of behavioural variation: (ii) strength of animal
 personality (behavioural repeatability), (iii) behavioural type
 (individual mean behaviour) and (iv) behavioural predictability
 (within-individual behavioural variation unrelated to environmental
 change). We found higher locomotor performance of juveniles from the
 vitamin-supplemented group (42.4% increase), irrespective of
 corticosterone treatment. While activity personality was present in all
 treatments, shelter use personality was present only in the
 vitamin-supplemented × corticosterone-treated treatment and risk-taking
 personality was present in corticosterone control treatments. Contrary to
 our expectations, behavioural type was not affected by our treatments,
 indicating that individual quality can affect behavioural strategies
 without affecting group-level mean behaviour. Behavioural predictability
 decreased in individuals with low climbing speed, which could be
 interpreted as a form of anti-predator strategy. Our results clearly
 demonstrate that maternal diet and corticosterone treatment have the
 potential to induce or hamper between-individual variation in different
 components of boldness, often in interactions.
DOI: 10.5061/dryad.hqbzkh1bj
title: Data from: Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

description: Our understanding of marine communities and their functions in an
 ecosystem relies on the ability to detect and monitor species
 distributions and abundances. Currently, the use of environmental DNA
 (eDNA) metabarcoding is increasingly being applied for the rapid
 assessment and monitoring of aquatic species. Most eDNA metabarcoding
 studies have either focused on the simultaneous identification of a few
 specific taxa/groups or have been limited in geographical scope. Here we
 employed eDNA metabarcoding to compare beta diversity patterns of complex
 pelagic marine communities in tropical coastal shelf habitats spanning the
 whole Caribbean Sea. We screened 68 water samples using a universal
 eukaryotic COI barcode region and detected highly diverse communities,
 which varied significantly among locations, and proved good descriptors of
 habitat type and environmental conditions. Less than 15% of eukaryotic
 taxa were assigned to metazoans, most DNA sequences belonged to a variety
 of planktonic ‘protists’, with over 50% of taxa unassigned at the phylum
 level, suggesting that the sampled communities host an astonishing amount
 of micro-eukaryotic diversity yet undescribed or absent from COI reference
 databases. Although such a predominance of micro-eukaryotes severely
 reduces the efficiency of universal COI markers to investigate vertebrate
 and other metazoans from aqueous eDNA, the study contributes to the
 advancement of rapid biomonitoring methods, and brings us closer to a full
 inventory of extant marine biodiversity.
description: Seawater was filtered using Millipore MCE filters 0.45 µm pore
 size and eDNA was extracted using MoBIO (DNEasy) PowerSoil DNA extraction
 kit. We used Leray-XT primers to amplify the Leray 313
 bp fragment of mitochondrial cytochrome c oxidase (COI) and sequenced it
 in an Illumina Miseq V3 2x250 bp. OBITools were used
 for paired-end assembly, demultiplexing and quality control. Chimeras were
 removed with uchime_denovo in VSearch. Swarm 2.0 with d=13 was used for
 clustering MOTUs. Ecotag was used for taxonomic assignment using custom
 reference databases for the COI Leray region. LULU was used for removing
 supernumerary MOTUs arising from pseudogenes. Singleton MOTUs were
 removed.
description: COI eDNA metabarcoding of filtered seawater
DOI: 10.5061/dryad.sn02v6x0w
title: Data from: Effects of land-use change on functional and taxonomic diversity of Neotropical bats

description: Human land-use changes are particularly extensive in tropical regions,
 representing one of the greatest threats to terrestrial biodiversity and a
 key research topic in conservation. However, studies considering the
 effects of different types of anthropogenic disturbance on the functional
 dimension of biodiversity in human-modified landscapes are rare. Here, we
 obtained data through an extensive review of peer-reviewed articles and
 compared 30 Neotropical bat assemblages in well-preserved primary forest
 and four different human-disturbed habitats in terms of their functional
 and taxonomic diversity. We found that disturbed habitats that are
 structurally less similar to primary forest (pasture, cropland and
 early-stage secondary forest) were characterized by a lower functional and
 taxonomic diversity, as well as community level-functional uniqueness.
 These habitats generally retained fewer species that perform different
 ecological functions compared to higher-quality landscape matrices, such
 as agroforestry. According to functional trait composition, different bat
 ensembles respond differently to landscape change, negatively affecting
 mainly gleaning insectivorous bats in pasture, narrow-range species in
 cropland, and heavier animalivorous bats in secondary forest. Although our
 results highlight the importance of higher-quality matrix habitats to
 support elevated functional and taxonomic bat diversity, the conservation
 of bat species that perform different ecological functions in the mosaic
 of human-modified habitats also depends on the irreplaceable conservation
 value of well-preserved primary forests. Our study based on a pooled
 analysis of individual studies provides novel insights into the effects of
 different human-modified habitats on Neotropical bat assemblages.
DOI: 10.5061/dryad.t4b8gthxm
title: Revisiting a landmark study-system: no evidence for a punctuated mode of evolution in Metrarabdotos

description: Is speciation generally a ‘special time’ in morphological evolution or are
 lineage splitting events just ‘more of the same’ where the end product
 happens to be two separate lineages? Data on evolutionary dynamics during
 anagenetic and cladogenetic events among closely related lineages within a
 clade are rare, but the fossil record of the bryozoan genus Metrarabdotos
 is considered a textbook example of a clade where speciation causes rapid
 evolutionary change against a backdrop of morphological stasis within
 lineages. Here, we point to some measurement theoretical and
 methodological issues in the original work on Metrarabdotos. We then
 reanalyze a subset of the original data that can be meaningfully
 investigated using similar quantitative statistical approaches as in the
 original studies. We consistently fail in finding variation in the
 evolutionary process during within-lineage evolution compared to
 cladogenetic events: Neither the rates of evolution, the strength of
 selection or the directions traveled in multivariate morphospace are
 different when comparing evolution within lineages and at speciation
 events in Metrarabdotos, and genetic drift cannot be excluded as a
 sufficient explanation for the morphological differentiation within
 lineages and during speciation. Although widely considered the best
 example of a punctuated mode of evolution, morphological divergence and
 speciation are not linked in Metrarabdotos.