cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15548479
title: TABLE 1 in Population structure of long-snout seahorse Hippocampus reidi in Southwestern Atlantic and implications for management

description: TABLE 1 | Molecular parameters of Hippocampus reidi populations and lineages/groups along the Brazilian coast. **In nuclear marker, the N number corresponds to alleles; PA = Pará; PI = Piauí; CE = Ceará; RN = Rio Grande do Norte; PB = Paraíba; PE = Pernambuco; AL = Alagoas; BA = Bahia; ES = Espírito Santo; RJ = Rio de Janeiro; SP = São Paulo; SC = Santa Catarina; NNE = Lineage formed by Northeast samples, except Bahia samples; BA = Group formed by Bahia samples; SSA = Lineage formed by South and Southeast samples, except Bahia samples; N = Sample size; H = Haplotype number; Hp = Private haplotypes (percentage in parenthesis); S = Polymorphic sites; h = Haplotype diversity; π = Nucleotide diversity; *significant P values (p <0.05).
MarkerLocationNHHpShΠFs de FuD de TajimamtDNAPA93030.6390.00121.1760.794PI3071 (1.45%)150.4620.0011-1.826-2.21*CE4181 (1.45%)80.6850.0013-1.896-0.65RN3071 (1.45%)70.4620.0007-3.527*-1.598*PB3052 (2.9%)80.3080.0007-1.309-1.876*PE3281 (1.45%)70.6880.0012-2.607-0.658AL4063 (4.35%)100.3590.0007-2.063-1.996*BA472823 (33.3%)450.9520.0059-11.742*-1.148ES4064 (5.8%)170.3910.00150.2927-1.868*RJ25149 (13.04%)280.920.0034-4.903*-1.784*SP761 (1.45%)180.9520.0049-0.9-1.313SC31118 (11.6%)210.8430.0025-2.287-1.538NNE2121715 (21.7%)290.5160.00098-9.9*-2.158*BA472823 (33.3%)450.9520.0059-11.742*-1.148SSE1033025 (36.2%)540.8710.0029-15.976*-2.135*Total3626954 (78.2%)940.8140.0048-24.735*-1.835*S7** (nuDNA)PA146060.7470.0043-0.6810.655PI605060.6480.00442.931.898CE765060.6070.00423.0531.791RN604060.6330.00444.231.905PB584060.670.00464.4122.089PE805060.6340.00433.2891.948AL785160.6490.00443.4412.101BA805050.6340.00342.1871.611ES823040.5760.00344.9982.448RJ427040.6840.0037-0.03042.552SP126040.8790.0033-1.7481.029SC403040.6680.00323.6081.815Total68211160.6840.00421.2342.742
description: Published as part of Queiroz-Brito, Maria Clara Gonçalves, Defavari, Gabriela Rocha, Rosa, Ierecê de Lucena & Torres, Rodrigo Augusto, 2024, Neotropical Ichthyology 22 (3) on page e 240027, DOI: 10.1590/1982-0224-2024-0027, http://zenodo.org/record/15548427
DOI: 10.5281/zenodo.15548481
title: TABLE 2 in Population structure of long-snout seahorse Hippocampus reidi in Southwestern Atlantic and implications for management

description: TABLE 2 | AMOVA of Hippocampus reidi testing different hypothesis by mitochondrial data. *Significant p values (p <0.05). BR: represents all sample sites in one single group; NNE represents PA, PI, CE, RN, PB, PE, AL populations; SES represents ES, RJ, SP, SC populations; BA represents Bahia population; ES represents Espírito Santo population.
HypothesisBR1)NNE 2)SES1)NNE+BA 2)SES1)NNE 2)SES+BA1)NNE 2)BA 3)SES1)NNE 2)BA 3)ES 4)SES1)NNE 2)BA+ES 3)SESVariation Source (%)Between groupsnuDNA -mtDNA -78.6660.5466.9667.1669.0766.54Between populations4.0259.982.9512.765.433.080.283.32Within populations95.9840.0218.3926.727.629.7630.6530.15Fixation indicesF SC--0.14*0.32*0.16*0.094*0.009*0.099*F ST0.04*0.59*0.82*0.73*0.72*0.7*0.7*0.7*F CT--0.79*0.61*0.67*0.67*0.69*0.67*
description: Published as part of Queiroz-Brito, Maria Clara Gonçalves, Defavari, Gabriela Rocha, Rosa, Ierecê de Lucena & Torres, Rodrigo Augusto, 2024, Neotropical Ichthyology 22 (3) on page e 240027, DOI: 10.1590/1982-0224-2024-0027, http://zenodo.org/record/15548427
DOI: 10.5281/zenodo.15548482
title: TABLE 2 in Population structure of long-snout seahorse Hippocampus reidi in Southwestern Atlantic and implications for management

description: TABLE 2 | AMOVA of Hippocampus reidi testing different hypothesis by mitochondrial data. *Significant p values (p <0.05). BR: represents all sample sites in one single group; NNE represents PA, PI, CE, RN, PB, PE, AL populations; SES represents ES, RJ, SP, SC populations; BA represents Bahia population; ES represents Espírito Santo population.
HypothesisBR1)NNE 2)SES1)NNE+BA 2)SES1)NNE 2)SES+BA1)NNE 2)BA 3)SES1)NNE 2)BA 3)ES 4)SES1)NNE 2)BA+ES 3)SESVariation Source (%)Between groupsnuDNA -mtDNA -78.6660.5466.9667.1669.0766.54Between populations4.0259.982.9512.765.433.080.283.32Within populations95.9840.0218.3926.727.629.7630.6530.15Fixation indicesF SC--0.14*0.32*0.16*0.094*0.009*0.099*F ST0.04*0.59*0.82*0.73*0.72*0.7*0.7*0.7*F CT--0.79*0.61*0.67*0.67*0.69*0.67*
description: Published as part of Queiroz-Brito, Maria Clara Gonçalves, Defavari, Gabriela Rocha, Rosa, Ierecê de Lucena & Torres, Rodrigo Augusto, 2024, Neotropical Ichthyology 22 (3) on page e 240027, DOI: 10.1590/1982-0224-2024-0027, http://zenodo.org/record/15548427
DOI: 10.5061/dryad.d51c5b02k
title: Populations of high-value predators reflect the traits of their prey dataset

description: The extent to which prey traits combine to influence the abundance of
 predators is still poorly understood, particularly for mixed predators in
 sympatry and in aquatic ecosystems. In this study, we characterise prey
 use and distribution in iconic bird (grey wagtails and Eurasian dippers)
 and fish species (brown trout and Atlantic salmon) to assess whether prey
 traits could predict populations of these four riverine predators.
 Specifically, we hypothesised that: (i) Prey key traits would predict
 predator populations more effectively than (ii) Diversity of prey traits,
 (iii) the taxonomic abundance or richness of prey (known as traditional or
 mass-effect types of biodiversity) or (iv) the prevailing environmental
 conditions. Combined predator population sizes were predicted better by a
 few key traits – specifically those revealing prey habitat use, size and
 drifting behaviour – than by prey diversity or prey trait diversity or
 environmental conditions. Our findings demonstrate that the complex
 relationships between prey assemblages and multiple predator species can
 be represented mechanistically when the key prey traits that govern
 encounter and consumption rates are identified. Given their apparent
 potential to reveal trophic relationships, and to complement more
 traditional measures of prey abundance, we advocate further development of
 trait-based approaches in predator-prey research.
DOI: 10.5061/dryad.rv15dv47j
title: Codes and data from: The effect of habitat choice on evolutionary rescue in subdivided populations

description: Evolutionary rescue is the process by which a population, in response to
 an environmental change, successfully avoids extinction through
 adaptation. In spatially structured environments, dispersal can affect the
 probability of rescue. Here, we model an environment consisting of patches
 that degrade one after another, and we investigate the probability of
 rescue by a mutant adapted to the degraded habitat. We focus on the
 effects of dispersal and of immigration biases. We find that the
 probability of evolutionary rescue can undergo up to three regions: (i)
 starting from low dispersal rates, it increases with dispersal; (ii) at
 intermediate dispersal rates, it decreases; (iii) finally, at large
 dispersal rates, the probability of rescue increases again with dispersal,
 except if mutants are too counter-selected in not-yet-degraded patches.
 The probability of rescue is generally highest when mutant and wild-type
 individuals preferentially immigrate into patches that have already
 undergone environmental change. Additionally, we find that mutants that
 will eventually rescue the population most likely first appear in
 non-degraded patches. Overall, our results show that habitat choice, when
 compared to the often studied unbiased immigration scheme, can
 substantially alter the dynamics of population survival and adaptation to
 new environments.
description: Codes and datasets for generating the figures in the main text
 and the Supplementary Information of the manuscript entitled "The
 effect of habitat choice on evolutionary rescue in subdivided
 populations" published in The American Naturalist.
description: For the codes to run on a cluster one can use the files run.sh
 and script.sh which can be found in every subfolder.
 The code for compiling the C++ files is in the header of the
 corresponding C++ file (GNU scientific library is used).
 All files can be found in a structured form (folders for each
 figures) at
 https://gitlab.com/pczuppon/evolutionary_rescue_and_dispersal
DOI: 10.5061/dryad.n8pk0p2tw
title: Results of CNN-based pollen analysis

description: Several datasets representing cross-validation of convoluted neural
 network (CNN) classification of pollen images. In each data file, one
 variable represents the pollen species (or pollen type when pollen are not
 identified to species level, but to a group of morphologically similar
 species represented by a type), and one the model predicted species. The
 remaining variables are the model likelihoods of the individual pollen
 grain belonging to a particular species. The maximum of these likelihoods
 will identify the predicted species. Each row in the datasets represent
 one pollen grain. An R-script to reproduce results in the paper is
 included.
DOI: 10.5061/dryad.nvx0k6drj
title: Emergence and repeatability of leadership and coordinated motion in fish shoals (Gasterosteus aculeatus)

description: Studies of self-organising groups like schools of fish or flocks of birds
 have sought to uncover the behavioural rules individuals use (local-level
 interactions) to coordinate their motion (global-level patterns). However,
 empirical studies tend to focus on short-term or one-off observations
 where coordination has already been established, or describe transitions
 between different coordinated states. As a result, we have a poor
 understanding of how behavioural rules develop and are maintained in
 groups. Here, we study the emergence and repeatability of coordinated
 motion in shoals of stickleback fish (Gasterosteus aculeatus). Shoals were
 introduced to a simple environment, where their spatio-temporal position
 was deduced via video analysis. Using directional correlation between fish
 velocities and wavelet analysis of fish positions, we demonstrate how
 shoals that are initially uncoordinated in their motion quickly transition
 to a coordinated state with defined individual leader-follower roles. The
 identities of leaders and followers were repeatable across two trials, and
 coordination was reached more quickly during the second trial, and by
 groups of fish with higher mean levels of activity. The rapid emergence of
 coordinated motion and repeatability of social roles in stickleback fish
 shoals may act to reduce uncertainty of social interactions in the wild,
 where individuals live in a system with high fission-fusion dynamics and
 non-random patterns of association.
DOI: 10.20350/digitalcsic/17908
title: Supplementary Material Assessment of Short-Term Sediment Deposition Patterns Along the Palamós Submarine Canyon (NW Mediterranean) Using 234Th

description: Table S1: Downcore dry bulk density and 234Th data, including mid-point measurement date, measured activity concentration (234Thmeas, 1st measurement), supported activity concentration (238U, 2nd measurement where 234Theq is equal to 238U) and mean value (±standard deviation) per station, excess activity concentration (234Thxs), excess inventory and weighted least squares (WLS) regression metrics used to calculate mixing rates
DOI: 10.5061/dryad.v15dv41vg
title: Inbreeding depression contributes to the maintenance of habitat segregation between closely related monkeyflower species

description: Incompletely reproductively isolated species often segregate into
 different microhabitats, even when they are able to survive and reproduce
 in both habitats. Longer term evolutionary factors may contribute to this
 lack of cross-habitat persistence. When reproductive interference reduces
 immigrant fitness, assortative mating, including self-fertilization,
 increases immigrants’ fitness in a single generation, but longer-term,
 inbreeding depression may reduce the chance of population persistence. Two
 California monkeyflower species repeatedly segregate into drier and wetter
 areas in their zone of sympatry. To test whether inbreeding depression may
 contribute to the maintenance of this segregation pattern, we transplanted
 outbred and successively inbred Mimulus guttatus and M. nudatus into their
 native habitats and heterospecific habitats. We measured germination,
 survival, and seed set and found that recurrent selfing reduced all
 aspects of fitness in both species, most strongly in foreign habitats. A
 simulation model, parameterized from the transplant experiment, found that
 inbreeding reduced fitness to such an extent that sequentially inbred
 populations of either species would be unable to persist in
 heterospecific-occupied habitats in the absence of continued gene flow.
 These results demonstrate that individual immigrants are unlikely to form
 persistent populations and thus, inbreeding depression contributes to the
 absence of fine-scale coexistence in this species pair.
description: Three datasets and two R scripts are included. The germination
 dataset was collected in a greenhouse and the reciprocal transplant
 dataset was collected at two field sites at the UC McLaughlin Reserve.
 Seeds were censused for germination in the greenhouse and a subset of
 germinants were transplanted into the field. In the field, tranplants were
 censused for survival and flowering. Fruit were collected at the end of
 the season, then seeds were counted from every transplant and categorized
 as viable or inviable based on morphology. The statistical analysis R
 code tests whether recurrent selfing reduces germination in the
 greenhouse, and survival and seed production in the field. The simulation
 R code is parameterized with data from the reciprocal transplant and
 simulates seed immigration with and without recurrent selfing as described
 in the manuscript. The simulation results dataset is the output of the
 simulation code for recurrently selfed and outcrossed seeds. 
description: MetadataS1.docx is a README file that describes the R code and
 data files, including column decscriptions for each data file.
DOI: 10.5061/dryad.79cnp5htt
title: Data from: Effects of hypoxia on the thermal physiology of a high-elevation lizard: Implications for upslope-shifting species

description: Montane reptiles are predicted to move to higher elevations in response to
 climate warming. However, whether upwards-shifting reptiles will be
 physiologically constrained by hypoxia at higher elevations remains
 unknown. We investigated the effects of hypoxic conditions on preferred
 body temperatures (Tpref) and thermal tolerance capacity of a montane
 lizard (Phrynocephalus vlangalii) from two populations on the
 Qinghai-Tibet Plateau. Lizards from 2600 m asl were exposed to O2 levels
 mimicking those at 2600 m (control) and 3600 m (hypoxia treatment).
 Lizards from 3600 m asl were exposed to O2 levels mimicking those at 3600
 m (control) and 4600 m (hypoxia treatment). The Tpref did not differ
 between the control and hypoxia treatments in lizards from 2600 m.
 However, lizards from 3600 m selected lower body temperatures when exposed
 to the hypoxia treatment mimicking the O2 level at 4600 m. Additionally,
 the hypoxia treatment induced lower critical thermal minimum (CTmin) in
 lizards from both populations, but did not affect critical thermal maximum
 (CTmax) in either population. Our results imply that upwards-shifting
 reptiles may be constrained by hypoxia if a decrease in Tpref reduces
 thermally-dependent fitness traits, despite no observed effect on their
 heat tolerance.
DOI: 10.5061/dryad.2z34tmpkv
title: Coral degradation impairs learning of non-predators by Whitetail damselfish

description: A prerequisite for effective antipredator responses is the ability of the
 prey to distinguish animals that pose a threat from those that do not.
 Prey often have efficient learning mechanisms to learn threats but
 learning to recognize nonpredators may be equally or more important.
 Moreover, the ability to generalize learned information is of key
 importance for prey animals. Prey take information they know about one
 species to make ‘educated guesses’ about the predatory/nonpredatory status
 of other unknown species. Here, we investigate the ability of Whitetail
 damselfish (Pomacentrus chrysurus) to learn the identity of non-predators
 and then generalize their responses to other unknown animals. Our work is
 completed within the context of unprecedented habitat degradation in reef
 ecosystems. When corals die, the remaining skeleton is colonized by algae,
 cyanobacteria and sessile invertebrates. These opportunistic colonists
 change the physical and chemical landscape of the reef and hence the
 background odour in which predator and non-predator recognition occurs.
 Our results indicated that Whitetail damselfish (Pomacentrus chrysurus)
 learn to classify Moonwrasse (Thalasomma lunare) as a non-predator through
 the process of latent inhibition, whereby the prey are repeatedly exposed
 to Moonwrasse odour multiple times in the absence of negative
 reinforcement. These fish subsequently generalized their nonpredator
 recognition to other unknown wrasse, but not distantly related fish. Of
 key importance was our finding that the patterns and extent of
 non-predator learning and generalization were dramatically altered in dead
 coral habitats. As predicted, prey that learned the Moonwrasse as a
 nonpredator in live coral environments did not subsequently respond to
 Moonwrasse when we tried to teach them Moonwrasse was a predator in live
 coral. However, this non-predator recognition was reduced in dead coral
 environments. Moreover, generalization completely failed when we changed
 from live to dead coral environments. Juvenile damselfishes need to
 rapidly catalogue the identity of unknown animals when they arrive at a
 reef. Changing background odours, that occur with changing tides and
 currents, means that prey need to learn non-predator identities separately
 in each water source. This cognitive challenge likely has significant
 survival consequence in a changing environment.
DOI: 10.5061/dryad.37pvmcvjq
title: Data from: Genotyping analysis of over 130,000 CIMMYT bread wheat breeding lines: A decade-long effort in optimizing wheat genotyping

description: A total of 130,247 bread wheat breeding lines from the year 2013-2023
 developed by the International Maize and Wheat Improvement Center (CIMMYT)
 were genotyped. We used genotyping-by-sequencing (GBS) to construct 636
 GBS libraries and sequenced them in the Illumina platform to generate
 FASTQ files. The key file consists of metadata such as sample name,
 flowcell, lane number, and barcode used for multiplexing samples. The
 FASTQ file of corresponding samples can be identified based on the
 library. The raw reads are available at the National Center for
 Biotechnology Information (NCBI) with BioProject accessions PRJNA498085
 (2013 – 2020 data), PRJNA901877 (2021), PRJNA901925 and PRJNA901462 (2022)
 and PRJNA1044425 (2023).
description: # Data from: Genotyping analysis of over 130,000 CIMMYT bread wheat
 breeding lines: A decade-long effort in optimizing wheat genotyping
 [https://doi.org/10.5061/dryad.37pvmcvjq](https://doi.org/10.5061/dryad.37pvmcvjq) ## Description of the data and file structure: 1\. This file consists of the name of FASTQ files generated after sequencing respective GBS libraries and also the SRA accession of the files. The Tassel GBS pipeline requires specific naming of FASTQ files for the analysis. So, the downloaded FASTQ files from NCBI can be renamed to the respective file names as listed in column 'file_name_for_Tassel'. `SRA_fastq_files_CIMMYT_bread_wheat_breeding_lines_2013-2023.xlsx` 2\. This file has information about the samples. The Tassel GBS pipeline uses the first four columns to identify sequencing reads present in the FASTQ files. `key_file_of_CIMMYT_bread_wheat_breeding_lines_from_years_2013-2023.xlsx` 3\. The steps below shows on how to extract a subset of samples for the analysis: ``` a. Select all rows with the sample names and also include the header from File 2. b. Identify all GBS libraries to be downloaded from column "LibraryPlateID" of File 2. c. Based on GBS libraries (File 1), download FASTQ file (SRA accession) from NCBI. d. Compress and rename the FASTQ file to the respective filename (File 1). e. Use the key file from step a. and FASTQ files from step d. as inputs in the Tassel GBS pipeline. ``` 4\. The scripts to analyze the data: ``` chi2_quality_test.R fisher_quality_test.R genotype_count_vcf.pl get_SNP_1filter_passed.sh inbred_quality_test.R tassel_pipeline.sh ``` 5\. Genotype data of 130,247 bread wheat breeding lines in VCF and hapmat formats. ``` CIMMYT_Filtered.130K.GIDs.hmp.txt.zip CIMMYT_Filtered.130K.GIDs.vcf.gz ``` ## Version changes **18-Feb-2021:** Only abstract was modified. **04-Nov-2025:** Additonal data of the bread wheat breeding lines from the year 2021-2023 were added in the files 1 and 2. The scripts to process the sequencing data and filtering have been added. A complete genotype data of the CIMMYT bread wheat breeding lines from the year 2013-2023 have been added.
DOI: 10.5281/zenodo.18396652
title: THE PSYCHOLOGICAL AND EDUCATIONAL FUNCTION OF MUSIC AND SOUND DESIGN

description: Contemporary musical sound design plays a central role in shaping human emotional and cognitive processes. This article analyzes the psychological and pedagogical functions of music through concepts such as soundscape, timbre, rhythm, primary and secondary dynamic contrast, harmony–disharmony manipulation, and immersive audio systems. The study is intended for the theoretical and practical exploration of sound–music integration within a conservatory educational environment.
DOI: 10.5281/zenodo.18396653
title: THE PSYCHOLOGICAL AND EDUCATIONAL FUNCTION OF MUSIC AND SOUND DESIGN

description: Contemporary musical sound design plays a central role in shaping human emotional and cognitive processes. This article analyzes the psychological and pedagogical functions of music through concepts such as soundscape, timbre, rhythm, primary and secondary dynamic contrast, harmony–disharmony manipulation, and immersive audio systems. The study is intended for the theoretical and practical exploration of sound–music integration within a conservatory educational environment.
DOI: 10.6084/m9.figshare.30976894
title: The chromosome-level genome assembly of the Malus robusta .

description: Genome assembly and annotation of Malus×robusta. The dataset includes the chromosome-level genome sequence and its structural gene annotation.
DOI: 10.6084/m9.figshare.30976894.v2
title: Malus×robusta

description: Genome assembly and annotation of Malus×robusta. The dataset includes the chromosome-level genome sequence and its structural gene annotation.
DOI: 10.6084/m9.figshare.30976894.v3
title: The chromosome-level genome assembly of the Malus robusta .

description: Genome assembly and annotation of Malus×robusta. The dataset includes the chromosome-level genome sequence and its structural gene annotation.