cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7c04d
title: Data from: Validating the use of coloration patterns for individual recognition in the worm pipefish using a novel set of microsatellite markers

description: In studies of behaviour, ecology and evolution, identification of
 individual organisms can be an invaluable tool, capable of unravelling
 otherwise cryptic information regarding group structure, movement
 patterns, population size and mating strategies. The use of natural
 markings is arguably the least invasive method for identification.
 However, to be truly useful natural markings must be sufficiently variable
 to allow for unique identification, while being stable enough to permit
 long-term studies. Non-invasive marking techniques are especially
 important in fishes of the Family Syngnathidae (pipefishes, seahorses and
 seadragons), as many of these taxa are of conservation concern or used
 extensively in studies of sexual selection. Here, we assessed the
 reliability of natural markings as a character for individual
 identification in a wild population of Nerophis lumbriciformis by
 comparing results from natural markings to individual genetic assignments
 based on eight novel microsatellite loci. We also established a minimally
 invasive method based on epithelial cell swabbing to sample DNA. All
 pipefish used in the validation of natural markings, independently of sex
 or time between recaptures, were individually recognized through facial
 colouration patterns. Their identities were verified by the observation of
 the same multilocus genotype at every sampling event for each individual
 that was identified on the basis of natural markings. Successful
 recaptures of previously swabbed pipefish indicated that this process
 probably did not induce an elevated rate of mortality. Also, the recapture
 of newly pregnant males showed that swabbing did not affect reproductive
 behaviour.
description: Facial
 ImagesFacial images used for
 the individual identification of the worm pipefish. Each pipefish as two
 images (of the right and left side of the face) in each of the capture
 events.genotypesExcel table with obtained genotypes for the set of 8 microsatellites. Sample information (including sex, length and reference to photo files) is also provided.
DOI: 10.5061/dryad.4p41m
title: Data from: Reliability assessment of null allele detection: inconsistencies between and within different methods

description: Microsatellite loci are widely used in population genetic studies, but the
 presence of null alleles may lead to biased results. Here, we assessed
 five methods that indirectly detect null alleles and found large
 inconsistencies among them. Our analysis was based on 20 microsatellite
 loci genotyped in a natural population of Microtus oeconomus sampled
 during 8 years, together with 1200 simulated populations without null
 alleles, but experiencing bottlenecks of varying duration and intensity,
 and 120 simulated populations with known null alleles. In the natural
 population, 29% of positive results were consistent between the methods in
 pairwise comparisons, and in the simulated data set, this proportion was
 14%. The positive results were also inconsistent between different years
 in the natural population. In the null-allele-free simulated data set, the
 number of false positives increased with increased bottleneck intensity
 and duration. We also found a low concordance in null allele detection
 between the original simulated populations and their 20% random subsets.
 In the populations simulated to include null alleles, between 22% and 42%
 of true null alleles remained undetected, which highlighted that detection
 errors are not restricted to false positives. None of the evaluated
 methods clearly outperformed the others when both false-positive and
 false-negative rates were considered. Accepting only the positive results
 consistent between at least two methods should considerably reduce the
 false-positive rate, but this approach may increase the false-negative
 rate. Our study demonstrates the need for novel null allele detection
 methods that could be reliably applied to natural populations.
description: Genotypes_dataThe file Genotypes_data.zip contains two folders: Simulated_genotypes, Simulated_genotypes_subpopulations and one .csv file named Microtus_oeconomus_genotypes.csv
DOI: 10.5281/zenodo.18244044
title: Primary data – physicochemical properties of polyamide 12 powders before and after the doped radiation spheroidization process, NCN MINIATURA 8, Decision No. DEC-2024/08/X/ST8/0049
title: Dane podstawowe – właściwości fizykochemiczne proszków poliamidu 12 przed i po procesie sferoidyzacji radiacyjnej z domieszkowaniem, MINIATURA 8 NCN, nr DEC-2024/08/X/ST8/00491

description: This dataset provides the results of physicochemical property investigations for Polyamide 12 (PA12), intended for additive manufacturing via Powder Bed Fusion of Polymers technology. The collection encompasses experimental data for post-process and subjected to the radiation-induced spheroidization process powders dedicated for Powder Bed Fusion of Polymers. This work was developed as part of the NCN MINIATURA 8 project, No. DEC-2024/08/X/ST8/00491.
description: This dataset was developed as part of the **NCN MINIATURA 8** project (National Science Centre, Poland), 
Decision No: **DEC-2024/08/X/ST8/00491**.

## 1. Material Description
The studied material is **Polyamide 12 (PA12)**, a thermoplastic polymer dedicated to the **Powder Bed Fusion of Polymers (PBF-LB/P)** additive manufacturing technology.

## 2. Sample Nomenclature
Sample names are constructed using the following abbreviations:

* **PA12**: Polyamide 12 (Base material)
* **A**: Post-process powder (collected after the PBF process)
* **S**: Powder after the radiation-induced spheroidization process
* **CB**: Carbon Black (filler)
* **rGO**: Reduced Graphene Oxide (filler)
* **025**: 0.25 wt.% concentration of the filler
* **05**: 0.5 wt.% concentration of the filler

**Example:** `PA12_S_025_rGO` refers to a spheroidized PA12 powder with a 0.25% weight concentration of reduced graphene oxide.

## 3. Characterization Methods
The dataset includes results obtained using the following experimental methods (listed alphabetically):

* **DLD** – Dry Laser Diffraction (Particle size distribution analysis)
* **DM** – Digital Microscopy (Surface and particle morphology imaging)
* **DRS** – Diffuse Reflectance Spectroscopy (Optical properties and absorption)
* **DSC** – Differential Scanning Calorimetry (Thermal properties: melting and crystallization)
* **FT4** – FT4 Powder Rheometry (Powder flowability and bulk properties)
* **GPC** – Gel Permeation Chromatography (Molecular weight distribution)
* **RPA** – Revolution Powder Analysis (Dynamic powder flow characterization)
* **SEM** – Scanning Electron Microscopy (High-resolution morphological analysis)
* **XRD** – X-ray Diffraction (Crystallographic structure analysis)

## 4. Contact and Citation
For more information, please contact the corresponding author listed in the Zenodo metadata. 

If you use this dataset, please cite it using the DOI provided by Zenodo and acknowledge the NCN MINIATURA 8 project.
DOI: 10.5281/zenodo.18244043
title: Primary data – physicochemical properties of polyamide 12 powders before and after the doped radiation spheroidization process, NCN MINIATURA 8, Decision No. DEC-2024/08/X/ST8/0049
title: Dane podstawowe – właściwości fizykochemiczne proszków poliamidu 12 przed i po procesie sferoidyzacji radiacyjnej z domieszkowaniem, MINIATURA 8 NCN, nr DEC-2024/08/X/ST8/00491

description: This dataset provides the results of physicochemical property investigations for Polyamide 12 (PA12), intended for additive manufacturing via Powder Bed Fusion of Polymers technology. The collection encompasses experimental data for post-process and subjected to the radiation-induced spheroidization process powders dedicated for Powder Bed Fusion of Polymers. This work was developed as part of the NCN MINIATURA 8 project, No. DEC-2024/08/X/ST8/00491.
description: This dataset was developed as part of the **NCN MINIATURA 8** project (National Science Centre, Poland), 
Decision No: **DEC-2024/08/X/ST8/00491**.

## 1. Material Description
The studied material is **Polyamide 12 (PA12)**, a thermoplastic polymer dedicated to the **Powder Bed Fusion of Polymers (PBF-LB/P)** additive manufacturing technology.

## 2. Sample Nomenclature
Sample names are constructed using the following abbreviations:

* **PA12**: Polyamide 12 (Base material)
* **A**: Post-process powder (collected after the PBF process)
* **S**: Powder after the radiation-induced spheroidization process
* **CB**: Carbon Black (filler)
* **rGO**: Reduced Graphene Oxide (filler)
* **025**: 0.25 wt.% concentration of the filler
* **05**: 0.5 wt.% concentration of the filler

**Example:** `PA12_S_025_rGO` refers to a spheroidized PA12 powder with a 0.25% weight concentration of reduced graphene oxide.

## 3. Characterization Methods
The dataset includes results obtained using the following experimental methods (listed alphabetically):

* **DLD** – Dry Laser Diffraction (Particle size distribution analysis)
* **DM** – Digital Microscopy (Surface and particle morphology imaging)
* **DRS** – Diffuse Reflectance Spectroscopy (Optical properties and absorption)
* **DSC** – Differential Scanning Calorimetry (Thermal properties: melting and crystallization)
* **FT4** – FT4 Powder Rheometry (Powder flowability and bulk properties)
* **GPC** – Gel Permeation Chromatography (Molecular weight distribution)
* **RPA** – Revolution Powder Analysis (Dynamic powder flow characterization)
* **SEM** – Scanning Electron Microscopy (High-resolution morphological analysis)
* **XRD** – X-ray Diffraction (Crystallographic structure analysis)

## 4. Contact and Citation
For more information, please contact the corresponding author listed in the Zenodo metadata. 

If you use this dataset, please cite it using the DOI provided by Zenodo and acknowledge the NCN MINIATURA 8 project.
DOI: 10.5061/dryad.5ns57
title: Data from: Evolutionary origin of the Scombridae (tunas and mackerels): members of a Paleogene adaptive radiation with 14 other pelagic fish families

description: Uncertainties surrounding the evolutionary origin of the epipelagic fish
 family Scombridae (tunas and mackerels) are symptomatic of the
 difficulties in resolving suprafamilial relationships within Percomorpha,
 a hyperdiverse teleost radiation that contains approximately 17,000
 species placed in 13 ill-defined orders and 269 families. Here we find
 that scombrids share a common ancestry with 14 families based on (i)
 bioinformatic analyses using partial mitochondrial and nuclear gene
 sequences from all percomorphs deposited in GenBank (10,733 sequences) and
 (ii) subsequent mitogenomic analysis based on 57 species from those
 targeted 15 families and 67 outgroup taxa. Morphological heterogeneity
 among these 15 families is so extraordinary that they have been placed in
 six different perciform suborders. However, members of the 15 families are
 either coastal or oceanic pelagic in their ecology with diverse modes of
 life, suggesting that they represent a previously undetected adaptive
 radiation in the pelagic realm. Time-calibrated phylogenies imply that
 scombrids originated from a deep-ocean ancestor and began to radiate after
 the end-Cretaceous when large predatory epipelagic fishes were selective
 victims of the Cretaceous-Paleogene mass extinction. We name this clade of
 open-ocean fishes containing Scombridae “Pelagia” in reference to the
 common habitat preference that links the 15 families.
description: 1n2n3acRnTn data
 set3rd codon positions AC
 converted. See README.txt for partition setting following RAxML
 format.07_ocean124ac3.phy1n2n3nRnTn data setAll codon positions included. See README.txt for partition setting following RAxML format.05_ocean124all.phy1n2nRnTn data set3rd codon positions excluded. See README.txt for partition setting following RAxML format.09_ocean124no3.phyaaRnTn data setProtein-coding genes are converted into amino acid sequences. See README.txt for partition setting following RAxML format.12_ocean124aart.nexATP6 data set used in bioinformatic analysis391 species included.ocean391_AT6.phyCO1 data set used in bioinformatic analysis3163 species includedocean3163_CO1.phyCYB data set used in bioinformatic analysis3045 species includedocean3045_CYB.phyND1 data set used in bioinformatic analysis363 species includedocean363_ND1.phyND2 data set used in bioinformatic analysis1309 species includedocean1309_ND2.phyND4 data set used in bioinformatic analysis237 species includedocean237_ND4.phyrag1 data set used in bioinformatic analysis1078 species includedocean1078_rag1.phyrag2 data set used in bioinformatic analysis642 species includedocean642_rag2.phyrhod data set used in bioinformatic analysis792 species includedocean792_rhod.phy
DOI: 10.5061/dryad.h3k4n
title: Data from: Improving accuracy of DNA diet estimates using food tissue control materials and an evaluation of proxies for digestion bias

description: Ecologists are increasingly interested in quantifying consumer diets based
 on food DNA in dietary samples and high-throughput sequencing of marker
 genes. It is tempting to assume that food DNA sequence proportions
 recovered from diet samples are representative of consumer's diet
 proportions, despite the fact that captive feeding studies do not support
 that assumption. Here, we examine the idea of sequencing control materials
 of known composition along with dietary samples in order to correct for
 technical biases introduced during amplicon sequencing and biological
 biases such as variable gene copy number. Using the Ion Torrent PGM©, we
 sequenced prey DNA amplified from scats of captive harbour seals (Phoca
 vitulina) fed a constant diet including three fish species in known
 proportions. Alongside, we sequenced a prey tissue mix matching the seals’
 diet to generate tissue correction factors (TCFs). TCFs improved the diet
 estimates (based on sequence proportions) for all species and reduced the
 average estimate error from 28 ± 15% (uncorrected) to 14 ± 9%
 (TCF-corrected). The experimental design also allowed us to infer the
 magnitude of prey-specific digestion biases and calculate digestion
 correction factors (DCFs). The DCFs were compared with possible proxies
 for differential digestion (e.g. fish protein%, fish lipid%) revealing a
 strong relationship between the DCFs and percent lipid of the fish prey,
 suggesting prey-specific corrections based on lipid content would produce
 accurate diet estimates in this study system. These findings demonstrate
 the value of parallel sequencing of food tissue mixtures in diet studies
 and offer new directions for future research in quantitative DNA diet
 analysis.
description: Tissue mix DNA amplicon
 pool (.fastq)This file contains the
 DNA sequences and quality scores that resulted from Ion Torrent amplicon
 sequencing of a fish tissue mixture that matched the seal diet in the
 study. See manuscript text for details.PDZA_mix.fastqSeal scat DNA amplicon pool (.fastq)This file contains the DNA sequences and quality scores that resulted from Ion Torrent amplicon sequencing of 48 individually amplified seal scats from the feeding trial. The harbour seals were fed: capelin (Mallotus villosus) (40%), Pacific herring (Clupea pallasii) (30%), chub mackerel (Scomber japonicus) (15%), and market squid (Loligo opalescens) (15%). See text for details.PDZA_scats.fastqFigure_DataData used to create figures 2-5. See Readme file for details
DOI: 10.5061/dryad.k501d
title: Data from: Recent diversification of a marine genus (Tursiops spp.) tracks habitat preference and environmental change

description: Understanding the evolution of diversity and the resulting systematics in
 marine systems is confounded by the lack of clear boundaries in oceanic
 habitats, especially for highly mobile species like marine mammals.
 Dolphin populations and sibling species often show differentiation between
 coastal and offshore habitats, similar to the pelagic/littoral or benthic
 differentiation seen for some species of fish. Here we test the hypothesis
 that lineages within the polytypic genus Tursiops track past changes in
 the environment reflecting ecological drivers of evolution facilitated by
 habitat release. We used a known recent time point for calibration (the
 opening of the Bosphorus) and whole mitochondrial genome (mitogenome)
 sequences for high phylogenetic resolution. The pattern of lineage
 formation suggested an origin in Australasia and several early divisions
 involving forms currently inhabiting coastal habitats. Radiation in
 pelagic environments was relatively recent, and was likely followed by a
 return to coastal habitat in some regions. The timing of some nodes
 defining different ecotypes within the genus clustered near the two most
 recent interglacial transitions. A signal for an increase in
 diversification was also seen for dates after the last glacial maximum.
 Together these data suggest the tracking of habitat preference during
 geographic expansions, followed by transition points reflecting habitat
 shifts, which were likely associated with periods of environmental change.
description: Moura et al
 supplementary file 14Jul13online
 supplement
DOI: 10.15468/dl.kkp6ms
title: Occurrence Download

description: A dataset containing 112 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "Geometry POLYGON((-69.72371 19.24677,-69.60631 19.288,-69.61633 19.33971,-69.74304 19.31385,-69.72371 19.24677))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 112 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001597-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p7bryn
title: Occurrence Download

description: A dataset containing 630 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((66.84438 24.86097,74.98971 5.84437,79.90764 6.45557,77.75604 19.30993,74.37496 26.10952,66.84438 24.86097))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Crocodylia"
 ]
}

 The dataset includes 630 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001598-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sc5qmm
title: Occurrence Download

description: A dataset containing 2030 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Mimosa gracilis gracilis, Mimosa gracilis capillipes, Mimosa gracilis brevissima, Mimosa gracilis invisiformis, Mimosa gracilis longipes, Mimosa gracilis stipitata, Mimosa gracilis)"
 ]
}

 The dataset includes 2030 records from 109 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001596-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.22d26
title: Data from: The shape of modern tree reconstruction methods

description: One characteristic of inferred phylogenetic trees is their shape. Rooted
 binary trees are more balanced, or symmetric, to the extent that sister
 groups contain similar number of leaves. Premised on the idea that
 macroevolutionary processes may leave a strong signature in the shape of
 phylogenetic trees, inferred tree shapes can be compared to expectations
 under probabilistic models of speciation and extinction in an attempt to
 make macroevolutionary inferences (e.g. Harvey and Purvis, 1991;
 Kirpatrick and Slatkin, 1993; Guyer and Slowinski, 1993; Mooers and Heard,
 1997; Bortolussi et al., 2006).
description: SystBiol_TreeData.tarSystBiol_TreeDataFinal.tar.gzSupplementary MaterialsSupplementary materialsSupplementary_Materials.pdf
DOI: 10.5061/dryad.vm523
title: Data from: Morphological stasis in an ongoing gastropod radiation from Lake Malawi

description: Evolutionary processes leading to adaptive radiation regularly occur too
 fast to be accurately recorded in the fossil record but too slowly to be
 readily observed in living biota. The study of evolutionary radiations is
 thereby confronted with an epistemological gap between the timescales and
 approaches used by neontologists and paleontologists. Here we report on an
 ongoing radiation of extant Bellamya species (n = 4) from the African Rift
 Lake Malawi that provides an unusual opportunity to bridge this gap. The
 substantial molecular differentiation in this monophyletic Bellamya clade
 has arisen since Late Pleistocene megadroughts in the Malawi Basin caused
 by climate change. Morphological time-series analysis of a
 high-resolution, radiocarbon-dated sequence of 22 faunas spanning the
 Holocene documents stasis up to the middle Holocene in all traits studied
 (shell height, number of whorls, and two variables obtained from geometric
 morphometrics). Between deposition of the last fossil fauna (∼5 ka) and
 the present day, a drastic increase in morphological disparity was
 observed (3.7–5.8 times) associated with an increase in species diversity.
 Comparison of the rates of morphological evolution obtained from the
 paleontological time-series with phylogenetic rates indicates that the
 divergence in two traits could be reconstructed with the slow rates
 documented in the fossils, that one trait required a rate reduction
 (stabilizing selection), and the other faster rates (divergent selection).
 The combined paleontological and comparative approach taken here allows
 recognition that morphological stasis can be the dominant evolutionary
 pattern within species lineages, even in very young and radiating clades.
description: General
 datasetThis dataset contains
 all information for the analyses in the paper. Each line represents an
 individual, columns indicate metadata and variables, e.g. assemblage
 numbers, assemblage age, log-transformed measurements and Procrustes
 superimposition coordinates.VanBocxlaerHunt-Dataset.txtR-script for the analysesThe analyses by Van Bocxlaer & Hunt were performed in the free software environment R (www.r-project.org). This file contains the R script for all analyses. Please see the paper for specifications related to package versions used. Some analyses may require substantial computer power; solutions may be delayed with minutes up to about an hour depending on computer specifications.VanBocxlaerHunt-Rscript.RRandomly resolved phylogenetic treesThis file contains the data of 50,000 randomly resolved, time-scaled phylogenetic trees as generated from the code in the provided R-script file. Re-running the code will provide highly similar, but different results. The trees provided in this file are the exact trees that we used for the analyses described in the paper.VanBocxlaerHunt-PhyloTrees.csv