cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j9kd51ck7
title: Data from: Ecological character displacement among Nothobranchius annual killifishes in Tanzania

description: Divergent ecological character displacement (ECD) is the
 competition-driven divergence in resource use-related phenotypic traits
 between coexisting species. It is considered one of the primary drivers of
 ecological diversification and adaptive radiation. We analyzed phenotypic
 and ecological variation in two African annual killifish species of the
 genus Nothobranchius; N. eggersi and N. melanospilus in sympatry and N.
 melanospilus in allopatry. Our aim was to test if allopatric and sympatric
 populations of N. melanospilus differ morphologically from each other and
 from N. eggersi, and examine if these differences are consistent with the
 predictions of ECD. We find that sympatric N. melanospilus differ from
 allopatric N. melanospilus and differ from N. eggersi more strongly than
 the latter. Our data satisfy four criteria for demonstrating ECD:
 Differences in phenotypes between allopatric and sympatric N. melanospilus
 are greater than expected by chance; the divergence pattern between
 allopatric and sympatric N. melanospilus results from an evolutionary
 shift rather than from ecological sorting; morphological differences
 observed reflect differences in resource use and, lastly, sites of
 allopatry and sympatry do not differ in food resource availability or
 other ecological conditions. Our results suggest that competition is the
 main driver of the observed divergence between two N. melanospilus
 populations.
description: Fishes and invertebrates were collected from seasonal ponds in
 Tanzania.The dataset consist of measurements of fish morphological
 feature, stomach contents and collected invertebrates.
description: # Ecological character displacement among Nothobranchius annual
 killifishes in Tanzania
 The Dataset
 comprises of data used in the analysis and results parts of the manuscript
 entitled "Ecological character displacement among *Nothobranchius*
 annual killifishes in Tanzania" submitted to Evolution. ##
 Description of the data and file structure Fishes and invertebrates were
 collected from seasonal ponds in Tanzania. The dataset consists of
 measurements of fish morphological features, stomach contents, and
 collected invertebrates. Abbreviations M-A Melanopilus from allopatric
 ponds. M-S Melanospilus from sympatric source. E-S Eggersi from sympatric
 source. SL-Fish Standard Length JL-Fish Jaw Length ED-Fish Eye Diameter
 hard bodied crustaceans (HBC), insect larvae (INL), and soft-bodied
 crustaceans (SBC). Crustaceans includes : Copepoda, Cladocera,
 Conchostraca, and Ostracoda insect larvae Include: Coleoptera, Odonata,
 Ephemeroptera, Hymenoptera, Hemiptera, Culicidae, and Chironomidae In
 Invertebratesdata TYPE A- Allopatric Ponds In Invertebratesdata TYPE S-
 Sympatric ponds In fishdata: All the three measurements SL, JL and ED are
 in "mm"
DOI: 10.15468/sj8w5v
title: Arrhinolemur scalabrinii Ameghino, 1898, of the late Miocene - a taxonomic journey from the Mammalia to the Anostomidae (Ostariophysi: Characiformes)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Bogan, Sergio, Sidlauskas, Brian, Vari, Richard P., Agnolin, Federico (2012): Arrhinolemur scalabrinii Ameghino, 1898, of the late Miocene - a taxonomic journey from the Mammalia to the Anostomidae (Ostariophysi: Characiformes). Neotropical Ichthyology 10 (3): 555-560, DOI: 10.1590/S1679-62252012000300008, URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1679-62252012000300008&lng=en&tlng=en
DOI: 10.15468/dl.yv6w9d
title: Occurrence Download

description: A dataset containing 157 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leptodesmia congesta",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 157 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003861-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.x0k6djhs7
title: Data from: fish (eggs) out of water: evolutionary divergence in terrestrial embryonic plasticity in Trinidadian killifish

description: Research has shown that externally laid eggs are often responsive to
 environmental signals. How such embryonic plasticity evolves is unclear.
 In Trinidad, the killifish (Anablepsoides hartii) are found in communities
 with and without predators. Killifish inhabit shallower, ephemeral habitat
 in sites with predators. Such shifts increase the exposure of eggs to air
 and possible desiccation. We compared embryonic plasticity between
 communities by rearing eggs terrestrially on peat moss or in water. The
 timing of hatching did not differ between communities when eggs were
 reared in water. Eggs from sites with predators responded to terrestrial
 incubation by hatching significantly earlier compared to water reared
 eggs. These responses were weaker in sites with no predators. Such
 divergent trends show that the presence of predators is associated with
 shifts in embryonic plasticity. Our results provide new insights into the
 factors that favor the evolutionary transition between life on water vs.
 land.
description: These data were collected via egg incubation experiments that
 manipulated the duration of exposure to semi-terrestrial
 conditions.
description: # Data from: fish (eggs) out of water: evolutionary divergence in
 terrestrial embryonic plasticity in Trinidadian killifish --- This is one
 data file with two tabs. One for the 15-day air exposure experiments and
 the other for the 12-day air exposure experiments. ## Description of the
 Data and file structure Here is a guide to each tab: Tab 1: 15 day air
 exposure experiments Stream = focal rivers (AM = Arima, AP = Aripo)
 Population= fish community (HP=high predation, KO=killifish only sites)
 Family= male and female lineages used to produce eggs Day at egg hatching
 = egg development rate (i.e., no. of days before egg hatched) F length =
 female length (cm) F mass = female weight (g) Treatment = egg rearing
 conditions (peat moss or in water) Age at growth = age of the offspring
 when size was assessed Offsoring size = offspring weight on ~day 30 (g)
 The missing values ('n/a') for offpring size represent eggs that
 hatched but the subsequent larvae did not survive until day 30. Tab 2: 12
 day air exposure experiments Stream = focal rivers (AM = Arima, AP =
 Aripo) Population= fish community (HP=high predation, KO=killifish only
 sites) Family= male and female lineages used to produce eggs Day at egg
 hatching = egg development rate (i.e., no. of days before egg hatched) F
 length = female length (cm) F mass = female weight (g) ## Sharing/access
 Information Links to other publicly accessible locations of the data: Was
 data derived from another source? No
DOI: 10.15468/dl.3h3ddk
title: Occurrence Download

description: A dataset containing 1971 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Freshwater biodiversity of the Eastern Highlands of Zimbabwe: Assessing conservation priorities using primary species-occurrence data"
 ]
}

 The dataset includes 1971 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003862-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18405645
title: Correcting Citation Inflation via Bayesian Knowledge Integration: A Scalable Framework Validated on OpenAlex Data

description: This paper introduces the Bayesian Knowledge Integration Index (BKII), a novel bibliometric metric designed to evaluate the quality and interdisciplinary integration of scientific contributions while correcting for citation inflation and manipulative practices. BKII employs a hierarchical Bayesian model using Negative Binomial likelihood to handle overdispersed citation counts, integrated with Rao-Stirling diversity, entropy-based novelty measures, and NLP-derived functional citation weights. We validate BKII empirically on a representative sample of 10,000 publications from OpenAlex, demonstrating its superior ability to predict prestigious awards such as Nobel Prizes and Fields Medals with an ROC AUC of 0.89, compared to 0.80 for the h-index. Retrospective analyses on 50 Nobel laureates in Physics versus 50 matched non-laureates confirm BKII's enhanced discrimination. Through Monte Carlo simulations, agent-based modeling, sensitivity analyses, and comparisons with established metrics (h-index, g-index, i10-index, h5-index, CNCI, m-index, disruption index, innovation index, EDM, RCR) and MCMC implementations (Stan, PyMC, JAGS), we demonstrate BKII's superior robustness and predictive accuracy under various stress scenarios. The framework provides credible intervals, anomaly detection for citation cartels, and field-normalized scores, offering a reproducible tool for academic evaluations, funding decisions, and policy-making. Code and data processing scripts are available on GitHub for community verification. No external funding was received.
DOI: 10.5061/dryad.jq2bvq8h1
title: The Vitex trifolia complex of the Philippines

description: We successfully assembled the complete chloroplast genomes of five species
 belonging to the Vitex trifolia complex. Based on a detailed analysis of
 specimens, which combines molecular and morphological data, we propose
 reinstating V. elmeri Moldenke and delineating V. arvensis Gentallan,
 Sengun & M.B.Bartolome as a new species belonging to this complex.
 The new species is a putative hybrid between V. bicolor Willd and V.
 elmeri Moldenke. We also provided a taxonomic key to identify the five
 species belonging to the V. trifolia complex in the Philippines.
description: # *Vitex trifolia* complex 
 ## Description of the data and file structure These are the plastomes of
 the Vitex trifolia complex in FASTA format. ## Methods The DNA samples
 were extracted using a slightly modified CTAB protocol of Doyle and Doyle
 (1987). The DNA samples were sent to NovogeneAIT Genomics Singapore PTE
 LTD, Singapore, for sequencing using the HiSeq-PE150 platform (Illumina
 Inc., San Diego, CA, USA). This generated cleaned reads of approximately 2
 Gbp. The chloroplast genomes were assembled using GetOrganelle v1.7.5+
 (Jin et al., 2020).
DOI: 10.5061/dryad.wwpzgmsrm
title: New electronic evidence authentication and protection scheme based on lattice

description: The electronic evidence authentication and protection scheme is based on
 the lattice cryptosystem, and other illegal users or attackers are unable
 to obtain the original electronic evidence data in the whole process of
 the electronic evidence protection system, which well protects the
 security of the original electronic evidence and increases the overall
 security of the scheme.
description: # Algorithm computational complexity The electronic evidence
 authentication and protection scheme is based on the lattice cryptosystem,
 and other illegal users or attackers are unable to obtain the original
 electronic evidence data in the whole process of the electronic evidence
 protection system, which well protects the security of the original
 electronic evidence and increases the overall security of the scheme. The
 authentication sizes corresponding to different safety grade coefficients
 (such as 64bits, 128bits, 256bits and 512bits) can be calculated when the
 selected system parameter is n=512bits, q=2**64. The results are shown in
 the file named "the data of this article.xlsx". The algorithm
 authentication size corresponding to different safety grade coefficients
 of our proposed lat-tice-based cipher scheme and RSA and ECC
 authentication algorithms is given. As shown in the file named "the
 data of this article.xlsx" The meaning of "Safety grade
 coefficient " in this data file is as follows: a parameter of a
 security level, in which the higher the parameter, the more secure the
 scheme. The meaning of "RSA algorithm " in this data file is as
 follows: a widely used asymmetric cryptographic algorithm. The
 corresponding data below represent the computational complexity of the
 algorithm. The higher the numerical value, the higher the complexity, and
 the higher the security level of the scheme. The meaning of "ECC
 algorithm " in this data file is as follows: a widely used symmetric
 cryptographic algorithm. The corresponding data below represent the
 computational complexity of the algorithm. The higher the numerical value,
 the higher the complexity, and the higher the security level of the
 scheme. The meaning of "Our algorithm " in this data file is as
 follows: the scheme proposed in this paper. The corresponding data below
 represent the computational complexity of the algorithm. The higher the
 numerical value, the higher the complexity, and the higher the security
 level of the scheme.
DOI: 10.5061/dryad.x69p8czrh
title: Habitat quality and biological community responses to innovative hydropower plant installations at transverse in-stream structures

description: Ecological assessments of the effects of hydropower plants (HPPs) are
 often limited to aspects of entrainment, mortality, injuries, and passage
 of fish, whereas the effects on riverine habitats and biological
 communities in proximity to these structures are hardly documented. In
 this study, aquatic communities comprising fish, macroinvertebrates,
 macrophytes, and periphyton as well as physical and hydromorphological
 parameters were investigated in upstream and downstream river sections at
 five transverse structures at different seasons before and after the
 installation of an innovative HPP. At all study sites, significant
 differences in the aquatic community composition between the assessed
 upstream and downstream sections were found after HPP construction,
 indicating distinct serial discontinuity. Raising the damming target at
 the sites Großweil and Au deteriorated the habitat conditions in the
 upstream area close to the weir and presumably influenced in particular
 the macroinvertebrate community, where a significant decrease in the
 density of rheophilic mayfly, stonefly, and caddisfly larvae was observed
 after HPP construction. Synthesis and applications: The installation of
 different types of innovative HPPs has not improved the habitat conditions
 for rheophilic species, contrary to the promises raised by the developers
 of these concepts. Conversely, retrofitting existing weirs accompanied by
 further damming even significantly increased the effects of serial
 discontinuity and deteriorated the habitat conditions for rheophilic
 species in upstream sections. As evident from the findings of this study,
 habitat and biological community effects resulting from serial
 discontinuity should become better integrated into ecological assessments
 of HPP developments.
description: # Habitat quality and biological community responses to innovative
 hydropower plant installations at transverse in-stream structures
 The dataset comprises
 biotic (fish, macroinvertebrates, macrophytes, and periphyton) and abiotic
 data (physical and hydromorphological parameters) that were recorded in
 upstream and downstream river sections at five transverse structures at
 different seasons before and after the installation of an innovative
 hydropower plant. ## Description of the data and file structure The data
 are organised in cross tables, with the rows indicating the sampling sites
 and the sampling time and the columns indicating the taxa detected (biotic
 data) or the parameters measured (abiotic data). Column headers contain
 units for abiotic data. Abbreviations for abiotic parameters: * DO =
 dissolved oxygen * OW = open water * INT = interstitial zone * T = water
 temperature * EC = electric conductivity * EH = redox potential * CV =
 current velocity * depth = water depth * GSF = grain size fraction of the
 river bed * DG = geometric mean particle diameter * Δ = difference between
 values from open water samples and interstitial water
DOI: 10.5061/dryad.wpzgmsbvm
title: k-mer matrix Aegilops tauschii diversity panel (Open wild wheat consortium phase II) Part 2/3

description: Wild wheat relatives of bread wheat represent genetic diversity that can
 be used for wheat crop improvement. We generated a k-mer presence/absence
 matrix of over 920 accessions of the wild wheat Aegilops tauschii, the
 donor of the bread wheat D genome. This dataset was generated under the
 aegis of Phase II of the Open Wild Wheat Consortium
 (www.openwildwheat.org).
description: The full methods are available in the related publication.
description: # Population genomics of the wild wheat Aegilops tauschii (Open Wild Wheat
 Consortium) - k-mer matrix PART 2/3-
 [https://doi.org/10.5061/dryad.wpzgmsbvm](https://doi.org/10.5061/dryad.wpzgmsbvm) ## **Description of the data and file structure** *k*-mer presence/absence matrix for the *Aegilops tauschii* diversity panel of over 920 accessions, including genetically redundant accessions. Resequencing of the *Ae. tauschii* accessions: We generated short-read whole genome sequencing data for 350 *Ae. tauschii* accessions.  PCR-free paired-end libraries were constructed and sequenced on an Illumina Novaseq 6000 instrument, yielding a median 8.3-fold coverage per sample (ranging from 5.87 to 16.86-fold). *k*-mer matrix generation. We developed and implemented an optimised *k*-mer matrix workflow to generate a presence/absence *k*-mer matrix for large diversity panels ([https://github.com/githubcbrc/KGWASMatrix](https://github.com/githubcbrc/KGWASMatrix)). We counted *k*-mers (*k* = 51) in raw sequencing data for 350 accessions generated in this study, 306 accessions published by Gaurav et al. (2022), 275 accessions published by Zhou et al. (2021) and 24 accessions by Zhao et al. (2023). Accessions with less than 5-fold sequencing coverage were discarded to avoid affecting the *k*-mer count. *k*-mers were filtered by a minimum occurrence of six across accessions and a maximum occurrence of (N-6), being N the total number of accessions. Detailed information about this *k*-mer matrix is found in the related pre-print by Cavalet-Giorsa, Gonzalez-Munoz and Athiyannan et al. (2023) ([https://doi.org/10.1101/2023.11.29.568958](https://doi.org/10.1101/2023.11.29.568958)). The full *k*-mer matrix has a total size of ~729G and has been divided into 25 gzipped files. The full *k*-mer matrix is tab-delimited in which the first column contains 10,078,115,665 k-mers and the remaining columns show the presence (1) or absence (0) across the accessions that are listed in order in the matrix_acc945_samples_list.txt file found in part 1/3 (doi:10.5061/dryad.p5hqbzkvx). This dataset contains gzipped files 9 through 17 of the full *k*-mer matrix, as follow: 9_m.tsv.gz 10_m.tsv.gz 11_m.tsv.gz 12_m.tsv.gz 13_m.tsv.gz 14_m.tsv.gz 15_m.tsv.gz 16_m.tsv.gz 17_m.tsv.gz The first and third parts of the *k*-mer matrix are available in additional related DRYAD datasets: doi:10.5061/dryad.p5hqbzkvx doi:10.5061/dryad.wm37pvmvd
DOI: 10.5061/dryad.3ffbg79rb
title: Occurrence data of small rodent species from the Yamal peninsula (1958–2022)

description: Range shifts and changes in dominance of species in communities are among
 the major predicted impacts of climate change on ecosystems, supported by
 numerous modeling studies. While climate is changing particularly rapidly
 in the Arctic, little observational data is available to document
 predicted changes in the composition of communities, in particular from
 the large Russian tundra areas. Small rodents are a key component of
 tundra ecosystems implementing important ecological functions both as
 herbivores and as main prey for a whole guild of predators. Here we
 document changes over 60 years in occurrence of nine species of small
 rodents along a latitudinal gradient spanning from the forest-tundra
 ecotone to the high Arctic tundra on the Yamal Peninsula. All data were
 obtained using a single method: snap-trapping. In general, the occurrence
 of lemmings, specialized arctic endemics, decreased in the southern parts
 of the peninsula, whereas the occurrence of voles, representing boreal or
 wide-spread species, increased and expanded northwards. The occurrence of
 Siberian lemmings (Lemmus sibiricus) in particular declined over the whole
 latitudinal gradient and possibly disappeared from the southernmost zones,
 whereas collared lemmings (Dicrostonyx torquatus) declined significantly
 only in the forest tundra. The strongest increase was observed in the
 tundra zones for narrow-headed voles (Lasiopodomys gregalis), a
 wide-spread species inhabiting meadows and riparian habitats, and
 Middendorff’s voles (Alexandromys middendorffii), a primarily low Arctic
 species inhabiting waterlogged tundra. Both species also expanded their
 distribution range northwards during the last two decades. The observed
 changes might be due to the effect of several drivers of environmental
 change occurring in concert: climate warming both in winter and in summer,
 and increased human activity notably related to intensive reindeer herding
 and industrial development.
description: # Yamal small rodent occurrence
 Presented dataset include
 information about occurrence of small rodent species during trapping
 events in Yamal peninsula, north-west Siberia, Russia conducted in
 1958-2022. ## Description of the data and file structure The file entitled
 "Sokolova_et_al_Yamal_small_rodent_occurrence.xlsx" contains
 the: i) Trapping ID - code of particular trapping event; ii) coordinates
 (latitude and longitude) of the trapping event iii) bioclimatic tundra
 subzone for each trapping event iv) year of particular trapping event v)
 occurrence (presence - 1; absence - 0) of 8 small rodent species during a
 particular trapping event. The file contains all the data needed to
 reproduce Figures 1, 2, and 3 shown in Sokolova et al. (2024). It will
 also allow the user to reproduce Figures S1, S2, and S3. If you have any
 questions, please, feel free to contact us:
 [nasokolova@yandex.ru](mailto:nasokolova@yandex.r)
DOI: 10.5281/zenodo.18404248
title: cynodonichthys_frommi_spades_01.fasta.gz
DOI: 10.5281/zenodo.18404249
title: cynodonichthys_frommi_spades_01.fasta.gz