cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p2ngf1vp7
title: Sea freshening may drive the ecological impacts of emerging and existing invasive alien species dataset

description: Aim: The spread of invasive non-native species (INNS) will pose major
 threats to global biodiversity over the coming decades. However,
 predicting how key effects of climate change will influence the abilities
 of INNS to establish and exert ecological impact is a major challenge. One
 overlooked aspect of global change is the expected freshening of certain
 marine systems, which may interact with INNS and lead to drastic effects
 on community structure and stability. Location: Baltic Sea, Europe
 Methods: Here, using three predatory amphipod crustaceans, we
 experimentally assessed how salinity reduction may affect the impacts of
 the emerging INNS, Pontogammarus maeoticus, relative to an existing INNS,
 Gammarus tigrinus, and a trophically analogous native, Gammarus salinus.
 We quantified per capita impacts of the three species via the comparative
 functional response method (prey consumption over a range of prey
 densities) under a predicted seawater freshening scenario. We then
 combined amphipod functional responses with their life history traits to
 compare population-level relative impact potential (RIP) on prey of the
 three amphipod species across salinities. Results: Freshening
 substantially altered the predicted relative ecological impacts of both
 the INNS compared to the native. First, the functional responses of
 invasive P. maeoticus and G. tigrinus increased under freshening, while
 that of the native G. salinus decreased. Second, RIP became consistently
 higher for both the INNS compared to the native with increased freshening.
 Main conclusions: Our methods thus reveal potential for climate change via
 seawater freshening to drive large shifts in dominance and ecological
 impacts of INNS compared to natives. With the number of INNS introductions
 unlikely to saturate in the near future, we highlight the need to assess
 the impacts of potential future INNS, alongside established non-natives
 and native species, in combination with abiotic changes associated with
 climate change.
description: The dataset relates to a series of functional response
 experiments across two experimental salinities, featuring a native and two
 non-native amphipod crustacean species. The data was analysed using the
 Frair package in R.
description: Three species listed as G. tig (<em>Gammarus
 tigrinus</em> - established non-native), G. sal (<em>Gammarus
 salinus</em> - native) and P. mae (<em>Pontogammarus
 maeoticus</em> - potential future non-native). Density relates to
 the number of <em>Artemia franciscana</em> prey offered, with
 the five experimental salinities being 2, 4, 8, 16 and 32. Treatment of
 prey consumed, and prey consumed and wounded, outlined in published
 manuscript.
DOI: 10.1594/pangaea.915156
title: Acoustic borehole logging of MeBo sediment core GeoB23702-3

description: Logging was performed with the sea floor drill rig MARUM-MeBo70 in a borehole drilled with a 103 mm diameter bit. The 1343 Slimhole Memory Acoustic instrument developed by ANTARES Datasystems GmbH was used. The probe consists of 1 transmitter and two receivers in 0.9 and 1.0 m distance, respectively. Sound velocity in the formation was calculated from the time difference of signal arrival at both receivers using the waveform processing module of the Antares software GeoBase 6.22. The vertical resolution is about 10 cm. The accuracy is better than 10 m/s.
DOI: 10.1594/pangaea.915157
title: Acoustic borehole logging of MeBo sediment core GeoB23725-1

description: Logging was performed with the sea floor drill rig MARUM-MeBo70 in a borehole drilled with a 103 mm diameter bit. The 1343 Slimhole Memory Acoustic instrument developed by ANTARES Datasystems GmbH was used. The probe consists of 1 transmitter and two receivers in 0.9 and 1.0 m distance, respectively. Sound velocity in the formation was calculated from the time difference of signal arrival at both receivers using the waveform processing module of the Antares software GeoBase 6.22. The vertical resolution is about 10 cm. The accuracy is better than 10 m/s.
DOI: 10.1594/pangaea.915158
title: Acoustic borehole logging of MeBo sediment core GeoB23730-1

description: Logging was performed with the sea floor drill rig MARUM-MeBo70 in a borehole drilled with a 103 mm diameter bit. The 1343 Slimhole Memory Acoustic instrument developed by ANTARES Datasystems GmbH was used. The probe consists of 1 transmitter and two receivers in 0.9 and 1.0 m distance, respectively. Sound velocity in the formation was calculated from the time difference of signal arrival at both receivers using the waveform processing module of the Antares software GeoBase 6.22. The vertical resolution is about 10 cm. The accuracy is better than 10 m/s.
DOI: 10.5061/dryad.fbg79cnsr
title: RepeatModeler and RepeatMasker output files

description: Transposable elements (TEs) are selfish genomic parasites whose ability to
 spread autonomously is facilitated by sexual reproduction in their hosts.
 If hosts become obligately asexual, TE frequencies and dynamics are
 predicted to change dramatically, but the long-term outcome is unclear.
 Here, we test current theory using whole-genome sequence data from eight
 species of bdelloid rotifers, a class of invertebrates in which males are
 thus far unknown. Contrary to expectations, we find a variety of active
 TEs in bdelloid genomes, at an overall frequency within the range seen in
 sexual species. We find no evidence that TEs are spread by cryptic
 recombination or restrained by unusual DNA repair mechanisms. Instead, we
 find that that TE content evolves relatively slowly in bdelloids and that
 gene families involved in RNAi-mediated TE suppression have undergone
 significant expansion, which might mitigate the deleterious effects of
 active TEs and compensate for the consequences of long-term asexuality.
description: TEs and other repeats were identified using the RepeatModeler and
 RepeatMasker pipelines. For each sample, a <i>de novo
 </i>repeat library was generated directly from the assembled
 nucleotides using RepeatModeler2 (Flynn et al., 2020) and combined with a
 database of 12,662 protostome repeats from Repbase v23.08 (Bao et al.,
 2015) and 278 additional TEs manually curated from the <i>A. vaga
 </i>genome (Flot et al., 2013). Repeats and TEs were then detected
 and classified using RepeatMasker v4.1.0 (Smit et al., 2013).
DOI: 10.1594/pangaea.915159
title: Acoustic borehole logging of MeBo sediment core GeoB23731-1

description: Logging was performed with the sea floor drill rig MARUM-MeBo70 in a borehole drilled with a 103 mm diameter bit. The 1343 Slimhole Memory Acoustic instrument developed by ANTARES Datasystems GmbH was used. The probe consists of 1 transmitter and two receivers in 0.9 and 1.0 m distance, respectively. Sound velocity in the formation was calculated from the time difference of signal arrival at both receivers using the waveform processing module of the Antares software GeoBase 6.22. The vertical resolution is about 10 cm. The accuracy is better than 10 m/s.
DOI: 10.1594/pangaea.956414
title: Organic matter and gel particles of Maria S. Merian cruise MSM85

description: The discrete biogeochemical measurements from RV Maria S. Merian MSM85 sampled for dissolved organic matter, microbial cell abundances and gel particles. The parameters include POC/PON, DOC/TDN, microbial cell abundances, gel particle concentrations like TEP and CSP. The samples were aquired within 5-2700 m of the Greenland Sea between 61 N to 77 N and 40 W to 4 W. The data was collected on board MSM85 from 27th July 2018-11th August 2019. The water collection occured using a CTD and laboratory methods varied by parameter. POC/PON was analysed using CHNS-O Elemental Analyser, DOC/TDN was analysed using TOC-VCSH, cell abundance (phytoplankton, bacteria, viral) was analysed using flow cytometery, gel particles were analysed colorimetrically using a spectrophotometer. The purpose of data collection was to understand spatial variability of organic mater and associated dynamics of the microbial loop.
DOI: 10.5061/dryad.qnk98sfdr
title: Long term butterfly trip species presence data with list lengths

description: These data were used as part of a study analyzing the patterns of changing
 phenology and abundance. Species day of year observations were analyzed
 using quantile regression (of the 0.1 and 0.9
 quantiles) of over years. Species abundance trends were
 measured using list length analysis, the result being the annual change in
 the proportion of trips on which a species was observed. Both
 phenology and abundance metrics were correlated and analyzed to understand
 thier potential relationship. Please refer to the manuscript, appendix,
 and metadata for more information.
description: Data were collected by skilled volunteer observers alone or in
 small groups. The number of each species seen on each outing was recorded,
 as was the date, observers, and location. Each file contains data for a
 species of butterfly which can be identified by its four letter code (e.g.
 'MONA' = Monarch <i>Danaus plexippus</i>: see
 'SPECIESCODES.csv', which includes the code, common name,
 scientific name, that the species was included or combined with another
 due to similarities or changes in reporting, classifications for voltinism
 and range type relative to the latitude of Boston, MA).
 Each trip was assigned retroactively. A 'trip'
 was considered a single observation, or set of observations, made by a
 single person, or the same set of people, on a single day in a single year
 at a certain location (within a single township). Each row of each file
 consitutes a single trip and for each trip the following are
 included: 'listlength', the list length of a
 trip (i.e. the total number of species were observed on this
 trip) 'present', whether the species was
 observed on that trip 'listyear', the year of
 the trip 'yearday', the numeric day of year
 of the trip (i.e. 1 = Jan. 1st, and 365 = Dec. 31st)
 'listplace', a numeric code corresponding to the
 township in which the trip occurred (see 'TOWNSHIPS.csv' which
 has only the towns and the corresponding codes)
description: Data were cleaned prior to processing though there remain some
 'NA' values.
DOI: 10.1594/pangaea.973021
title: Macro-nutrients data set from Expedition PS131, ATWAICE

description: Here we present a fully quality controlled macro-nutrient data set from analyses carried out onboard the RV Polarstern during the expedition PS131 ATlantic WAter pathways to the ICE in the Nansen Basin and Fram Strait (ATWAICE). The expedition took place from 27 June to 17 August 2022, starting and ending in Bremerhaven, Germany. Analyses of nitrate plus nitrite, nitrite, phosphate, silicate, total nitrogen and total phosphorus were carried out using a Seal Analytical AA500 segmented continuous flow nutrient autoanalyser as part of the Pelagic Biogeochemistry (Nutrients and net community production) Team activities (Grant-No AWI_PS131_06). The rationale as well as details of sampling and analysis can be found in the associated cruise report (https://doi.org/10.57738/BzPM_0770_2023).
DOI: 10.1594/pangaea.978022
title: Time series data of environmental parameters in the water column of shallow lakes at the Attenborough Nature Reserve (2006-2013)

description: Temperature, dissolved oxygen, pH, calcium ions, total phosphorus, total suspended solids, and chlorophyll-a were measured monthly from May 2006 until August 2013 in the water column of six gravel pit shallow lakes (Beeston, Church, Clifton, Coneries, Tween, and Main) located at the Attenborough Nature Reserve, UK (52.883, -1.233). Temperature, dissolved oxygen, and pH were measured at 0.5 m depth using a YSI 600QS-O-M multiparameter attached to a 650MDS data logger during the daytime (09:00-17:00). The remaining parameters were quantified in depth-integrated water samples. Total phosphorus was measured via a standard colorimetric technique, and calcium ions were measured via ion chromatography following filtration through a pre-weighted Whatman GF/C filter paper (1.2 μm pore size). Total suspended solids were quantified by weighing after filtration, and chlorophyll-a was measured by spectrophotometric analysis. See all the details in Cross et al. 2014.
DOI: 10.1594/pangaea.978462
title: Time series data of flow of River Erewash (2006-2013)

description: Flow rates of the river Erewash were quantified monthly from May 2006 until August 2013. The mean monthly discharge of the river was calculated from measurements taken at 30-minute intervals using an Ultraflux UF322 CO ultrasonic flowmeter situated a short distance upstream from where the river enters the gravel pit Coneries Pond (52.897, -1.245) at the Attenborough Nature Reserve. The data were collected to study the influence of river discharge and rainfall on the ecology and biogeochemistry of lakes connected to the river Erewash. See all details in Cross et al., 2014 (doi:10.1127/fal/2014/0573).
DOI: 10.5061/dryad.wh70rxwkw
title: Data from: Dispersal limitations and long-term persistence drive differentiation from haplotypes to communities within a tropical sky-island: evidence from community metabarcoding

description: Neutral theory proposes that dispersal stochasticity is one of the main
 drivers of local diversity. Haplotypes-level genetic variation can now be
 efficiently sampled from across whole communities, thus making it possible
 to test neutral predictions from the genetic to species-level diversity,
 and higher. However, empirical data is still limited, with the few studies
 to date coming from temperate latitudes. Here, we focus on a tropical
 mountain within the Transmexican Volcanic Belt to evaluate spatially
 fine-scale patterns of arthropod community assembly to understand the role
 of dispersal limitation and landscape features as drivers of diversity. We
 sampled whole-communities of arthropods for eight orders at a spatial
 scale ranging from 50 m to 19 km, using whole community metabarcoding. We
 explored multiple hierarchical levels, from individual haplotypes to
 lineages at 0.5, 1.5, 3, 5, 7.5% similarity thresholds, to evaluate
 patterns of richness, turnover, and distance decay of similarity with
 isolation-by-distance and isolation-by-resistance (costs to dispersal
 given by landscape features) approaches. Our results showed that distance
 and altitude influence distance decay of similarity at all hierarchical
 levels. This holds for arthropod groups of contrasting dispersal
 abilities, but with different strength depending on the spatial scale. Our
 results support a model where local-scale differentiation mediated by
 dispersal constraints, combined with long-term persistence of lineages, is
 an important driver of diversity within tropical sky islands.
description: Please, See Material & Methods.
description: <strong>Data to use in scripts of metabarcoding
 arthropods</strong> This dataset includes the
 sequences aligned, ASVs tables and ASVs with Threshold generated from 42
 whole-communities of biodiversity soups in Nevado de Toluca. For
 additional information on the sample codes and scripts please see at
 Git-hub
 repository https://github.com/AliciaMstt/Multihierarchical_NevadoToluca.
 For the raw data please see at SRA project: PRJNA743572.
 <strong>Data content:</strong>
 `1AlignedSeq`: contains the results of
 `0.4Searching_Stop_Codons.txt`. This file contents each ASV dataset was
 aligned in Geneious for searching codon stops. After, each fasta file you
 can use in `0.5to_get_ASV_tables.sh`script.
 `2ASVs_Table`: contains the results of the
 `0.5to_get_ASV_tables.sh` analysis. Each community table was generated
 with read-counts (haplotype abundance) of each retained ASV for the eight
 orders by matching ASVs against the complete collection of reads. After,
 each ASV tables you can use in
 `0.6to_get_UPGMAtree_GMYC_MH_lineages_All.r` and
 `3.to_get_conservative_threhold_on_original_all.r`
 `3ASVThresholdCommunities`: contains all matrix tables used in
 `4.to_get_Diversity_All.r` and
 `6.to_get_BetaDiversity_DistanceDecay_IBD_IBR.r`scripts.
DOI: 10.1594/pangaea.978491
title: Time series of carbon sedimentation rates and C/N ratios resolved monthly from sediment traps in shallow lakes at the Attenborough Nature Reserve (2006-2013)

description: Total sedimentation rates, organic and inorganic carbon sedimentation rates, and C:N ratios were measured monthly from May 2006 until August 2013. Data were collected in sediment traps deployed at the deepest points of six gravel pit shallow lakes (Beeston, Church, Clifton, Coneries, Tween, and Main) at the Attenborough Nature Reserve, UK (52.883, -1.233). All collected sediment was homogenized and freeze-dried before analysis. Total sedimentation rates were estimated as follows: total sedimentation rate = (sediment weight/area sediment trap)/deployment time. The total carbon and nitrogen content were measured in subsamples of the sediments collected in the traps on an elemental analyzer (vario ISOTOPE select) in elemental CN measuring mode. Inorganic carbon was removed from subsamples of the sediments through an acidification treatment to quantify total organic carbon. Inorganic carbon content was estimated as the difference between total carbon measured before and after acidification. Organic and inorganic carbon sedimentation rates were calculated based on the percentage of organic or inorganic carbon relative to the total sedimentation rates. Organic carbon and nitrogen masses were converted to molar masses to calculate the C:N ratios. See all details in Franco-Cisterna et al. under revision in L&O.
DOI: 10.1594/pangaea.979398
title: Age determination of microbial carbonates deposited during the Holocene in the South Atlantic

description: The data refer to the geochemical and isotopic characterization of microbial carbonate in the shallow platform of the South Atlantic Ocean, Espírito Santo - Brazil. The determination of 14C activity was performed in Accelerator Mass Spectrometry (AMS) 14C dating at the Poznań Radiocarbon Laboratory. The determination of 14C activity was performed on 06 samples in Accelerator Mass Spectrometry (AMS) 14C dating at the Poznań Radiocarbon Laboratory (Linick et al., 1989). Background corrections were applied based on measurements of 14C-free calcite. Radiocarbon ages were calculated using the conventional radiocarbon age method (Stuiver and Polach, 1977) and calibrated using the CALIB REV8.20 software (Stuiver and Reimer, 1993). Calibration curves from Cabo Frio (RJ) and Guarapari (ES) were employed, with Delta R values -40.0 ± 17 and 29 ± 53 (Heaton et al., 2020; Alves et al., 2021). All dated samples were assigned a standard deviation of ±30 to ±35 years (2σ).
description: The study was carried out between 2021 and 2023 on the beach of Castelhanos in a carbonate bank to analyze the depositional dynamics throughout the Holocene. The occurrence of microbial carbonates in the open marine environment is uncommon globally, configuring an excellent proxy for the reconstitution of relative variations in sea level and paleoclimate.
DOI: 10.1594/pangaea.979497
title: δ13C and δ18O isotopic analyses of microbial carbonates deposited during the Holocene in the South Atlantic

description: The data refer to the geochemical and isotopic characterization of microbial carbonate in the shallow platform of the South Atlantic Ocean, Espírito Santo - Brazil. Carbon and oxygen isotope analysis fractions (δ¹³C and δ¹⁸O) were measured on six carbonate laminate samples using isotope ratio mass spectrometry (IRMS) on a Thermo Fisher Scientific Delta V Advantage instrument. Approximately 0,4-0,6 mg of carbonate was reacted with 100% phosphoric acid at 72ºC to release CO2 gas. International standards (NBS18, NBS19, IAEA-CO-1, IAEA-CO-8, IAEA-CO-9, and IAEA-603) were used for calibration. The analytical precision for δ13C and δ18O was better than 0,01% and 0,25%, respectively. Isotopic values are reported in delta notation (‰) relative to the Vienna Pee Dee Belemnite (VPDB) standard.
description: The study was carried out between 2021 and 2023 on the beach of Castelhanos in a carbonate bank to analyze the depositional dynamics throughout the Holocene. The occurrence of microbial carbonates in the open marine environment is uncommon globally, configuring an excellent proxy for the reconstitution of relative variations in sea level and paleoclimate.
DOI: 10.1594/pangaea.979556
title: Geochemical analyses of microbial carbonates deposited during the Holocene in the South Atlantic

description: The data refer to the geochemical and isotopic characterization of microbial carbonate in the shallow platform of the South Atlantic Ocean, Espírito Santo - Brazil. Geochemical and isotopic analyses were conducted at the LAMIR Institute of the Universidade Federal do Paraná (LAMIR Institute-UFPR). Major element concentrations were determined in three pulverized samples using X-ray fluorescence (XRF) spectrometry on a Panalytical Axios Max instrument with a 4 kV Rhodium tube. Samples were fused with lithium tetraborate/lithium metaborate and analyzed as fused beads. Results were reported as oxide weight percentages (e.g., SiO₂, CaO, MgO).
description: The study was carried out between 2021 and 2023 on the beach of Castelhanos in a carbonate bank to analyze the depositional dynamics throughout the Holocene. The occurrence of microbial carbonates in the open marine environment is uncommon globally, configuring an excellent proxy for the reconstitution of relative variations in sea level and paleoclimate.
DOI: 10.5061/dryad.xksn02vdp
title: Data for: Infectious disease and sickness behaviour: tumour progression affects interaction patterns and social network structure in wild Tasmanian devils

description: Infectious diseases, including transmissible cancers, can have a broad
 range of impacts on host behaviour, particularly in the latter stages of
 disease progression. However, the difficulty of early diagnoses makes the
 study of behavioural influences of disease in wild animals a challenging
 task. Tasmanian devils (Sarcophilus harrisii) are affected by a
 transmissible cancer, devil facial tumour disease (DFTD), in which tumours
 are externally visible as they progress. Using telemetry and
 mark-recapture data sets, we quantify the impacts of cancer progression on
 the behaviour of wild devils by assessing how interaction patterns within
 the social network of a population change with increasing tumour load.
 DFTD negatively influences devils’ likelihood of interaction within their
 network, an effect which increases with increasing tumour load. Infected
 devils were more active within their network late in the mating season, a
 pattern with repercussions for DFTD transmission. Our study provides a
 rare opportunity to quantify and understand the behavioural feedbacks of
 disease in wildlife and how they may affect transmission and population
 dynamics in general.
description: This data was collected using proximity loggers to record
 Tasmanian devil interactions over a 6 month period, whilst also tracking
 their DFTD infection.
DOI: 10.15468/dl.z2552k
title: Occurrence Download

description: A dataset containing 134 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "DatasetKey is one of (Arachnomorpha collection of the Royal Museum for Central Africa, Museum of Comparative Zoology, Harvard University, Ohio State Acarology Laboratory (OSAL), Ohio State University)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "TaxonKey is Ornithodoros moubata"
 ]
}

 The dataset includes 134 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002600-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.