cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tq09m
title: Data from: Genetic regulatory network motifs constrain adaptation through curvature in the landscape of mutational (co)variance

description: Systems biology is accumulating a wealth of understanding about the
 structure of genetic regulatory networks, leading to a more complete
 picture of the complex genotype-phenotype relationship. However, models of
 multivariate phenotypic evolution based on quantitative genetics have
 largely not incorporated a network-based view of genetic variation. Here
 we model a set of two-node, two-phenotype genetic network motifs, covering
 a full range of regulatory interactions. We find that network interactions
 result in different patterns of mutational (co)variance at the phenotypic
 level (the M-matrix), not only across network motifs but also across
 phenotypic space within single motifs. This effect is due almost entirely
 to mutational input of additive genetic (co)variance. Variation in M has
 the effect of stretching and bending phenotypic space with respect to
 evolvability, analogous to the curvature of space-time under general
 relativity, and similar mathematical tools may apply in each case. We
 explored the consequences of curvature in mutational variation by
 simulating adaptation under divergent selection with gene flow. Both
 standing genetic variation (the G-matrix) and rate of adaptation are
 constrained by M, so that G and adaptive trajectories are curved across
 phenotypic space. Under weak selection the phenotypic mean at
 migration-selection balance also depends on M.
description: Code and simulation
 outputThis tar.gz file
 contains directories with R code and simulation output for all figures and
 data described in the paper. See the README.pdf file for a full
 description of contents.Hether_Hohenlohe_Evolution.tar.gz
DOI: 10.5061/dryad.b451g
title: Data from: Metamorphosis revealed: time-lapse three-dimensional imaging inside a living chrysalis

description: Studies of model insects have greatly increased our understanding our
 animal development. Yet they are limited in scope to this small pool of
 model species: a small number of representatives for a hyperdiverse group
 with highly varied developmental processes. One factor behind this narrow
 scope is the challenging nature of traditional methods of study, such as
 histology and dissection, which can preclude quantitative analysis and do
 not allow the development of a single individual to be followed. Here we
 use high resolution computed tomography to overcome these issues to 3D
 image numerous lepidopteran pupae throughout their development. The
 resulting models are presented in figures and supplementary videos taken
 for a single individual throughout development. They provide new insight
 and details of lepidotperan metamorphosis, and allow the measurement of
 tracheal and gut volume. Furthermore, this study demonstrates early and
 rapid development of the tracheal system – while unresolved in the
 caterpillar, tracheae become visible in scans just 12 hours after
 pupation. This suggests that there is less remodelling of the tracheal
 system than previously expected, and is methodologically important because
 the tracheal system is an often-understudied character systems in
 development. In the future this form of CT-scanning could allow faster and
 detailed developmental studies on a wider range of taxa than is presently
 possible.
description: Supplementary material,
 S1A
 video showing 3D models of the chrysalis and its internal anatomy on every
 day it was scanned during development. The external morphology (i.e. pupal
 cuticle) and then internal anatomy (tracheal system, gut and air lumen)
 are shown for day one through a 360° rotation. Stills of day four, and
 seven showing internal anatomy are then followed by a rotation at day ten,
 a still of day thirteen, and then rotations of both day fourteen
 (internal) and day sixteen (external anatomy). We believe these animations
 demonstrate the power of 3D models when studying complex morphologies such
 as those of the tracheal system.Supplementary material,
 S2This video comprises the
 radiographs from each scan (i.e. the two-dimensional X-ray projection,
 rather than the digital visualization. Particularly apparent are the
 mid-gut and development of air sacs, as well as movement of the internal
 anatomy during each scan.Supplementary material,
 S3An
 excel fine containing volume data for the different organ systems in these
 models, coupled with graphs showing the change in both tracheal and gut
 volume as a percentage of chrysalis volume throughout
 development.Supplementary material,
 S4High resolution copies
 of figures 1,2, and 3.Supplementary material,
 S5Avizo surfaces of the
 models created from CT scans at days 1,4,7,10,13,14 and 16, used for
 figures 1–3.
DOI: 10.5061/dryad.218g3
title: Data from: Rungia sinothailandica sp. nov. (Acanthaceae) from China and Thailand

description: Rungia sinothailandica (Acanthaceae), a new species from Yunnan, China and
 Chiang Rai, Thailand is described and illustrated. A colour plate, line
 drawing and distribution map of R. sinothailandica are provided. Rungia
 sinothailandica is similar to R. pinpienensis H. S. Lo, but differs in the
 broadly ovate sterile bracts and obovate-elliptic fertile bracts, the
 crispate and tawny bracts margin, the 2-lobed upper lip of the corolla and
 puberulent capsule. It is also similar to R. burmanica (C. B. Clarke) B.
 Hansen, but is easily distinguished by pubescent stems and leaves, the
 cymbiform-oblong bracteoles and the 2-lobed upper lip of corolla.
description: Dryad（Rungia
 sinothailandica）Pollen and seed
 morphology, a colour plate, line drawing and distribution map of R.
 sinothailandica.
DOI: 10.5061/dryad.3hr2c
title: Data from: A migratory northern ungulate in the pursuit of spring: jumping or surfing the green wave?

description: The Forage Maturation Hypothesis (FMH) states that herbivores migrate
 along a phenological gradient of plant development in order to maximize
 energy intake. Despite strong support for the FMH, the actual relationship
 between plant phenology and ungulate movement has remained enigmatic. We
 linked plant phenology (MODIS-NDVI) and space use of 167 migratory and 78
 resident red deer (Cervus elaphus) using a space-time-time matrix of
 "springness", defined as the instantaneous rate of green-up
 (IRG). Consistent with the FMH, migrants experienced substantially greater
 access to early plant phenology than residents. Deer were also more likely
 to migrate in areas where migration led to greater gains in springness.
 Rather than "surfing the green wave" during migration, migratory
 red deer moved rapidly from the winter to the summer range, thereby
 "jumping the green wave". However, migrants, and to a lesser
 degree residents, did track phenological green-up through parts of the
 growing season by making smaller-scale adjustments in habitat use. We
 conclude that, whereas in some systems migration itself is a way to surf
 the green wave, in others it may simply be a means to re-connect with
 phenological spring at the summer range.
description: red deer GPS
 dataGPS data for 294 red
 deer monitored between 2002 and 2010 in Norway.reddeerGPSdata.txt
DOI: 10.5281/zenodo.18380591
title: Arquivos Vetoriais Doutorado

description: Dados vetoriais do doutorado



Cobertura da terra dos anos de 2002 e 2022

Qualidade Ambiental baseada na cobertura da terra de 2002 e 2022

Qualidade ambiental baseada no uso da terra de 2024/25

Mapeamento da cobertura vegetal de 2002 e 2025

Amostras de validação para o SAVI de 2022

outros
DOI: 10.5281/zenodo.18380592
title: Arquivos Vetoriais Doutorado

description: Dados vetoriais do doutorado



Cobertura da terra dos anos de 2002 e 2022

Qualidade Ambiental baseada na cobertura da terra de 2002 e 2022

Qualidade ambiental baseada no uso da terra de 2024/25

Mapeamento da cobertura vegetal de 2002 e 2025

Amostras de validação para o SAVI de 2022

outros
DOI: 10.5061/dryad.66gt5
title: Data from: Phylogenomic analyses of more than 4000 nuclear loci resolve the origin of snakes among lizard families

description: Squamate reptiles (lizards and snakes) are the most diverse group of
 terrestrial vertebrates, with more than 10 000 species. Despite
 considerable effort to resolve relationships among major squamates clades,
 some branches have remained difficult. Among the most vexing has been the
 placement of snakes among lizard families, with most studies yielding only
 weak support for the position of snakes. Furthermore, the placement of
 iguanian lizards has remained controversial. Here we used targeted
 sequence capture to obtain data from 4178 nuclear loci from ultraconserved
 elements from 32 squamate taxa (and five outgroups) including
 representatives of all major squamate groups. Using both concatenated and
 species-tree methods, we recover strong support for a sister relationship
 between iguanian and anguimorph lizards, with snakes strongly supported as
 the sister group of these two clades. These analyses strongly resolve the
 difficult placement of snakes within squamates and show overwhelming
 support for the contentious position of iguanians. More generally, we
 provide a strongly supported hypothesis of higher-level relationships in
 the most species-rich tetrapod clade using coalescent-based species-tree
 methods and approximately 100 times more loci than previous estimates.
description: 36 taxa RAxML (Fig.
 S2)36_taxa_infile_reduced_RAxML.txt37 taxa RAxML (Fig. S3)37_taxa_infile_reduced_RAxML.txt36 taxa ASTRAL alignments (Fig. S1)4715 UCE alignmentsASTRAL_36_taxa_4715_alignments.zip36 taxa ASTRAL best trees (Fig. S1)4715 best treesASTRAL_36_taxa_4175_best_trees.zip37 taxa ASTRAL alignments (Fig. 1)4178 UCE alignmentsASTRAL_37_taxa_4178_alignments.zip37 taxa ASTRAL best trees (Fig. 1)4178 best treesASTRAL_37_taxa_4178_best_trees.zip
DOI: 10.5061/dryad.05qs7
title: Data from: Single nucleotide polymorphism discovery via genotyping by sequencing to assess population genetic structure and recurrent polyploidization in Andropogon gerardii

description: Premise of the study. Autopolyploidy, genome duplication within a single
 lineage, can result in multiple cytotypes within a species. Geographic
 distributions of cytotypes may reflect the evolutionary history of
 autopolyploid formation and subsequent population dynamics including
 stochastic (drift) and deterministic (differential selection among
 cytotypes) processes. Here, we used a population genomic approach to
 investigate whether autopolyploidy occurred once or multiple times in
 Andropogon gerardii, a widespread, North American grass with two
 predominant cytotypes. Methods. Genotyping-by-sequencing was used to
 identify single nucleotide polymorphisms (SNPs) in individuals collected
 from across the geographic range of A. gerardii. Two independent
 approaches to SNP calling were used: the reference-free UNEAK pipeline and
 a reference-guided approach based on the sequenced Sorghum bicolor genome.
 SNPs generated using these pipelines were analyzed independently with
 genetic distance and clustering. Key results. Analyses of the two SNP
 datasets showed very similar patterns of population-level clustering of A.
 gerardii individuals: a cluster of A. gerardii individuals from the
 southern Plains, a northern Plains cluster, and a western cluster.
 Groupings of individuals corresponded to geographic localities regardless
 of cytotype: 6x and 9x individuals from the same geographic area clustered
 together. . Conclusions. SNPs generated using reference-guided and
 reference-free pipelines in A. gerardii yielded unique subsets of genomic
 data. Both datasets suggest that the 9x cytotype in A. gerardii likely
 evolved multiple times from 6x progenitors across the range of the
 species. Genomic approaches like GBS and diverse bioinformatics pipelines
 used here facilitate evolutionary analyses of complex systems with
 multiple ploidy levels.
description: McAllister_Miller_Andropogon_gerardii_UNEAK_SNPsZipped VCF file containing SNPs called using UNEAK bioinformatic pipeline in 190 Andropogon gerardii accessionsMcAllister.Miller.all.mergedUNEAKSNPs.vcf.gzMcAllister.Miller.all.mergedRefGuidedSNPs.vcfZipped VCF file containing SNPs called via alignment of GBS reads from 190 Andropogon gerardii accessions to the Sorghum bicolor genome.McAllister_Miller_Locality_Ploidy_InfoThis file includes locality and ploidy level inforomation for each specimen included in both SNP files in this dataset
DOI: 10.5061/dryad.3023m
title: Data from: Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddies the water

description: Antarctic krill (Euphausia superba; hereafter krill) are an incredibly
 abundant pelagic crustacean which has a wide, but patchy, distribution in
 the Southern Ocean. Several studies have examined the potential for
 population genetic structuring in krill, but DNA-based analyses have
 focused on a limited number of markers and have covered only part of their
 circum-Antarctic range. We used mitochondrial DNA and restriction
 site-associated DNA sequencing (RAD-seq) to investigate genetic
 differences between krill from five sites, including two from East
 Antarctica. Our mtDNA results show no discernible genetic structuring
 between sites separated by thousands of kilometres, which is consistent
 with previous studies. Using standard RAD-seq methodology, we obtained
 over a billion sequences from &gt;140 krill, and thousands of variable
 nucleotides were identified at hundreds of loci. However, downstream
 analysis found that markers with sufficient coverage were primarily from
 multicopy genomic regions. Careful examination of these data highlights
 the complexity of the RAD-seq approach in organisms with very large
 genomes. To characterize the multicopy markers, we recorded sequence
 counts from variable nucleotide sites rather than the derived genotypes;
 we also examined a small number of manually curated genotypes. Although
 these analyses effectively fingerprinted individuals, and uncovered a
 minor laboratory batch effect, no population structuring was observed.
 Overall, our results are consistent with panmixia of krill throughout
 their distribution. This result may indicate ongoing gene flow. However,
 krill's enormous population size creates substantial panmictic
 inertia, so genetic differentiation may not occur on an ecologically
 relevant timescale even if demographically separate populations exist.
description: 1 RAD-seq project info
 V22_Unique_RAD_TagsSequences of the unique RAD tags3a_BSP_pipeline_logParameters used to generate BAM/SAM files4 Variant call format files V2Variant call format files derived from the RAD sequencing5_VCF_extract_filesData extracted from Variant Call Format files6_R_code_count_PCAData and R code for principal component analysis (PCA) of the count data from the ‘Core Dataset’7_MtDNA_sequencesMtDNA sequence data for 142 krill. Two fragments were sequenced: 655 bp Cytochrome c Oxidase subunit I (COI) and 569 bp NADH Dehydrogenase subunit 1 (ND1).Extra_Figure5_SequencesSequences of the RAD tags used to produce trees in Figure 5 of the paper (FASTA format)Figure 5 sequences.zip
DOI: 10.5061/dryad.jh0gs15j
title: Data from: The trouble with isolation by distance

description: The genetic population structure of many species is characterised by a
 pattern of isolation by distance (IBD): due to limited dispersal,
 individuals that are geographically close tend to be genetically more
 similar than individuals that are far apart. Despite the ubiquity of IBD
 in nature, many commonly used statistical tests are based on a null model
 that is completely non-spatial, the Island model. Here, I argue that
 patterns of spatial autocorrelation deriving from IBD present a problem
 for such tests as it can severely bias their outcome. I use simulated data
 to illustrate this problem for two widely used types of tests: tests of
 hierarchical population structure and the detection of loci under
 selection. My results show that for both types of tests the presence of
 IBD can indeed lead to a large number of false positives. I therefore
 argue that all analyses in a study should take the spatial dependence in
 the data into account, unless it can be shown that there is no spatial
 autocorrelation in the allele frequency distribution that is under
 investigation. Thus, it is urgent to develop additional statistical
 approaches that are based on a spatially explicit null model instead of
 the non-spatial Island model.
description: Simulated genetic
 dataThis data package
 contains simulated genetic marker data (diallelic SNPs) that has been used
 to show the effects of Isolation by Distance on several widely used
 statistical inferences. The data has been simulate dusing the programs
 Marlin (Meirmans 2011) and QuantiNemo (Neuenschwander et al. 2008). For
 more information on the data contents and format, please consult the
 ReadMe file.
DOI: 10.5061/dryad.8kv2b20
title: Data from: Accurately quantifying the shape of birds' eggs

description: Describing the range of avian egg shapes quantitatively has long been
 recognised as difficult. A variety of approaches has been adopted, some of
 which aim to capture the shape accurately and some to provide intelligible
 indices of shape. The objectives here are to show that a (four-parameter)
 method proposed by Preston (1953) is the best option for quantifying egg
 shape, to provide and document an R program for applying this method to
 suitable photographs of eggs, to illustrate that intelligible shape
 indices can be derived from the summary this method provides, to review
 shape indices that have been proposed, and to report on the errors
 introduced by using photographs of eggs at rest rather than horizontal.
description: programs and test
 dataPrograms Preston.R and
 Indices.R, mentioned in supplementary material of the paper, to calculate
 the Preston parameters and then indices from that output. The zip file
 also contains test data and brief user guides for each
 program.programs.zipSupplementary-Material2.html 3d-plotdynamic 3d-plot illustrating the three indices Pointedness, Elongation and Polar Asymmetry for three species (Uria aalge, Uria lomvia, Alca torda)Supplementary-Material2.htmlData and AnalysisContains the R script (Analysis.R) which computes everything in the article, and the data sets used. Also contains the Rmarkdown file (Supplementary-Material2.Rmd) which produces the 3-d plot in Supplementary-Material2.htmlAnalysis.zip
DOI: 10.5061/dryad.t3t7p
title: Data from: Dynamical state transitions into addictive behaviour and their early-warning signals

description: The theory of critical transitions in complex systems (ecosystems,
 climate, etc.), and especially its ability to predict abrupt changes by
 early-warning signals based on analysis of fluctuations close to tipping
 points, is seen as a promising avenue to study disease dynamics. However,
 the biomedical field still lacks a clear demonstration of this concept.
 Here, we used a well-established animal model in which initial alcohol
 exposure followed by deprivation and subsequent reintroduction of alcohol
 induces excessive alcohol drinking as an example of disease onset.
 Intensive longitudinal data (ILD) of rat drinking behaviour and locomotor
 activity were acquired by a fully automated drinkometer device over 14
 weeks. Dynamical characteristics of ILD were extracted using a multi-scale
 computational approach. Our analysis shows a transition into addictive
 behaviour preceded by early-warning signals such as instability of
 drinking patterns and locomotor circadian rhythms, and a resultant
 increase in low frequency, ultradian rhythms during the first week of
 deprivation. We find evidence that during prolonged deprivation, a
 critical transition takes place pushing the system to excessive alcohol
 consumption. This study provides an adaptable framework for processing ILD
 from clinical studies and for examining disease dynamics and early-warning
 signals in the biomedical field.
description: Foo et al. 2017-
 ILD
DOI: 10.5061/dryad.f3sm9
title: Data from: Genomics and telemetry suggest a role for migration harshness in determining overwintering habitat choice, but not gene flow, in anadromous Arctic Char

description: Migration is a ubiquitous life history trait with profound evolutionary
 and ecological consequences. Recent developments in telemetry and
 genomics, when combined, can bring significant insights on the migratory
 ecology of non-model organisms in the wild. Here, we used this integrative
 approach to document dispersal, gene flow and potential for local
 adaptation in anadromous Arctic Char from six rivers in the Canadian
 Arctic. Acoustic telemetry data from 124 tracked individuals indicated
 asymmetric dispersal, with a large proportion of fish (72%) tagged in
 three different rivers migrating up the same short river in the fall.
 Population genomics data from 6,136 SNP markers revealed weak, albeit
 significant, population differentiation (average pairwise FST = 0.011) and
 asymmetric dispersal was also revealed by population assignments.
 Approximate Bayesian Computation simulations suggested the presence of
 asymmetric gene flow, although in the opposite direction to that observed
 from the telemetry data, suggesting that dispersal does not necessarily
 lead to gene flow. These observations suggested that Arctic Char home to
 their natal river to spawn, but may overwinter in rivers with the shortest
 migratory route to minimize the costs of migration in non-breeding years.
 Genome scans and genetic-environment associations identified 90 outlier
 markers putatively under selection, 23 of which were in or near a gene. Of
 these, at least four were involved in muscle and cardiac function,
 consistent with the hypothesis that migratory harshness could drive local
 adaptation. Our study illustrates the power of integrating genomics and
 telemetry to study migrations in non-model organisms in logistically
 challenging environments such as the Arctic.
description: batch_1_miss25MigrantsRepAcousHistSexRem_9jun2016.recodeVCF file containing the genotypes for the baseline samples EXCLUDING potential migrants (total N = 273 individuals; see table 1 and manuscript for details of which sites were considered baseline and how the migrants were identified) at 6136 SNP markers retained after quality filters described in the manuscript.batch_1_miss25RepAcousHistSexRem_7jun2016.recodeVCF file containing the genotypes for the baseline samples INCLUDING potential migrants (total N = 318 individuals; see table 1 and manuscript for details of which sites were considered baseline and how the migrants were identified) at 6136 SNP markers retained after quality filters described in the manuscript.Data_6136filteredSNPs_allIndividualsVCF file containing genotype data at all 6136 SNP markers retained after quality filters and for all individuals retained for analyses (i.e. excluding individuals with more than 25% missing data; total N = 391).batch_1_miss25SexRepRem_7jun2016.recode.vcf