cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vj134s0
title: Data from: Grow where you thrive, or where only you can survive? An analysis of performance curve evolution in a clade with diverse habitat affinities

description: Performance curves are valuable tools for quantifying the fundamental
 niches of organisms and testing hypotheses about evolution, life history
 trade-offs, and the drivers of variation in species' distribution
 patterns. Here, we present a novel Bayesian method for characterizing
 performance curves that facilitates comparisons among species. We then use
 this model to quantify and compare the hydrological performance curves of
 14 different taxa in the genus Lasthenia, an ecologically diverse clade of
 plants that collectively occupy a variety of habitats with unique
 hydrological features, including seasonally flooded wetlands called vernal
 pools. We conducted a growth chamber experiment to measure each
 taxon's fitness across five hydrological treatments that ranged from
 severe drought to extended flooding, and identified differences in
 hydrological performance curves that explain their associations with
 vernal pool and terrestrial habitats. Our analysis revealed that the
 distribution of vernal pool taxa in the field do not reflect their optimal
 hydrological environments: all taxa, regardless of habitat affinity, have
 highest fitness under similar hydrological conditions of saturated soil
 without submergence. We also found that a taxon's relative position
 across flood gradients within vernal pools is best predicted by the height
 of its performance curve. These results demonstrate the utility of our
 approach for generating insights into when and how performance curves
 evolve among taxa as they diversify into distinct environments. To
 facilitate its use, the modeling framework has been developed into an R
 package (https://github.com/silastittes/performr).
description: Growth chamber
 dataRaw growth chamber data
 for fourteen Lasthenia taxa analyzed in manuscript. Response variable:
 Inflor_biomass. Treatment levels, D (drought = 1), MD (minor drought = 2),
 B (benign = 3), MF (minor flood = 4), F (flood = 5). See paper and GitHub
 repository for details on how this file was filtered and parsed for
 downstream analyses.Pool depths_FINAL
 summary_REVISED.xlsLasthenia
 depthsField measures for
 average depth (cm) of taxon occurring within vernal
 pools.Pool
 depths_FINAL summary_REVISED.xlsName
 keyName key matching growth
 chamber taxa and tree tip labelsIsolate_Key.txtPosterior treesEach line of the file contains a posterior phylogeny generated using BALi-Phy (Suchard and Redelings 2006)C1.trees
DOI: 10.5061/dryad.818c434
title: Data from: Genomic parallelism and lack thereof in contrasting systems of three‐spined sticklebacks

description: Parallel evolution and the extent to which it involves gene reuse has
 attracted much interest. Whereas it has theoretically been predicted under
 which circumstances gene reuse is expected, empirical studies that
 directly compare systems showing high and low parallelism are rare.
 Three-spine stickleback (Gasterosteus aculeatus), where freshwater
 populations have been independently founded by ancestral marine
 populations, represent prime examples of phenotypic and genomic
 parallelism, but cases exist where parallelism is low. Based on RAD
 (Restriction site Associated DNA) sequencing we analyzed SNPs and
 chromosome inversions in populations in Denmark and Greenland showing low
 and high parallelism, respectively. We identified parallelism across
 freshwater populations in Greenland at genomic regions previously
 identified to be associated with marine-freshwater divergence. These same
 markers also separated Danish marine and freshwater sticklebacks, albeit
 to a weaker extent. Hence, parallelism was not absent in Denmark but
 possibly constrained by spatially and temporally varying selection.
 Divergence time estimates found one Danish freshwater population to be
 much older than the others. It also deviated strongly with respect to
 parallelism, and may represent earlier postglacial colonization based on a
 different pool of standing variation and eliciting different adaptive
 responses to freshwater conditions. This provides empirical support to
 previous suggestions that the time since replicate populations had access
 to a common pool of standing variation is a major factor determining gene
 reuse. Finally, sticklebacks in Greenland are expected to expand further
 North due to climate change. Based on the observed parallelism we discuss
 predictability of adaptive responses in newly established populations.
description: VCF file containing the
 SNPs obtained in this studybatch_1_filtered_auto_adj.vcfR script for finding inverted regions in a genome using population genomic datafindInvert-v2.r
DOI: 10.5061/dryad.m0m6r
title: Data from: Fruits of Juglandaceae from the Eocene of South America

description: Specimens of a new fruit taxon, Alatonucula ignis, from the early Eocene
 Laguna del Hunco flora of Chubut, Patagonia, Argentina, have
 characteristics consistent with assignment to Juglandaceae. Each fossil
 fruit consists of a nutlet with an attached wing that varies from unlobed
 to trilobed. One specimen clearly shows that the nutlet has a single
 locule partially subdivided into four chambers; its counterpart contains a
 four-lobed locule cast. The basally partitioned locule with lobed seed
 indicates that Alatonucula can be placed within Juglandaceae; the overall
 structure of the fruits suggests affinities to subfamily Engelhardioideae,
 which typically have fruits consisting of a nutlet attached to a trilobed
 wing. Parsimony analyses of a morphological matrix for extant and fossil
 Juglandaceae revised from a previously published study demonstrate that 1)
 Alatonucula groups with Engelhardioideae; and 2) Paleooreomunnea, an
 Eocene North American taxon that includes a fruit type with a trilobed
 wing, is within crown-group Engelhardioideae. Alatonucula, along with
 fossil juglandaceous pollen from the Paleogene of Patagonia, indicates
 that Juglandaceae may have had an unexpectedly early presence in South
 America. Furthermore, these fruits represent a Laurasian biogeographic
 signal in the Laguna del Hunco flora, which contrasts with the
 predominantly Australasian signal highlighted in previous studies.
description: Hermsen_Gandolfo_2D_3_panelsMovie showing a micro-CT scan of the locule cast of Alatonucula ignis preserved in the holotype specimen (MPEF-Pb 5090A). The movie starts at the base of the locule cast and moves apically. The specimen is shown in transverse and longitudinal sections. Imaging data were acquired through the Cornell University Biotechnology Resource Center.Hermsen_Gandolfo_2D_1_panelMovie showing a micro-CT scan of the locule cast of Alatonucula ignis preserved in the holotype specimen (MPEF-Pb 5090A). The movie starts at the base of the locule cast and moves apically. The specimen is shown in transverse section. Imaging data were acquired through the Cornell University Biotechnology Resource Center.Hermsen_Gandolfo_Juglandaceae_morphologyMorphological matrix for extant and fossil Juglandaceae.
DOI: 10.5061/dryad.7v222
title: Data from: Developmental mechanisms of stripe patterns in rodents

description: Mammalian colour patterns are among the most recognizable characteristics
 found in nature and can have a profound impact on fitness. However, little
 is known about the mechanisms underlying the formation and subsequent
 evolution of these patterns. Here we show that, in the African striped
 mouse (Rhabdomys pumilio), periodic dorsal stripes result from underlying
 differences in melanocyte maturation, which give rise to spatial variation
 in hair colour. We identify the transcription factor ALX3 as a regulator
 of this process. In embryonic dorsal skin, patterned expression of Alx3
 precedes pigment stripes and acts to directly repress Mitf, a master
 regulator of melanocyte differentiation, thereby giving rise to
 light-coloured hair. Moreover, Alx3 is upregulated in the light stripes of
 chipmunks, which have independently evolved a similar dorsal pattern. Our
 results show a previously undescribed mechanism for modulating spatial
 variation in hair colour and provide insights into how phenotypic novelty
 evolves.
description: De novo assembly of
 Rhabdomys pumilio transcriptome and detailed differential gene expression
 resultsThis dataset contains a
 fasta file, including the de novo assembly of Rhabdomys pumilio
 transcriptome (built from RNA-Seq data using the Trinity suite of de novo
 transcriptome assembly tools -
 https://github.com/trinityrnaseq/trinityrnaseq/wiki), as well as a tab
 separated text file indicating the gene annotations corresponding to each
 assembly contig, obtained by mapping the de novo assembly to the human
 reference transcriptome, as described in the manuscript. A third Excel
 file contains the detailed results of RNA-Seq differential gene expression
 study in skin obtained from three dorsal regions, as described in the
 manuscript.Rhabdomys_pumilio.zip
DOI: 10.15468/dl.y5grqv
title: Occurrence Download

description: A dataset containing 601 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bursera linanoe"
 ]
}

 The dataset includes 601 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000422-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kh0qh06
title: Data from: The International Tree-Ring Data Bank (ITRDB) revisited: data availability and global ecological representativity

description: Aim: The International Tree-Ring Data Bank (ITRDB) is the most
 comprehensive database of tree growth. To evaluate its usefulness and
 improve its accessibility to the broad scientific community, we aimed to:
 i) quantify its biases, ii) assess how well it represents global forests,
 iii) develop tools to identify priority areas to improve its
 representativity, and iv) make available the corrected database. Location:
 Worldwide. Time period: Contributed datasets between 1974 and 2017. Major
 taxa studied: Trees. Methods: We identified and corrected formatting
 issues in all individual datasets of the ITRDB. We then calculated the
 representativity of the ITRDB with respect to species, spatial coverage,
 climatic regions, elevations, need for data update, climatic limitations
 on growth, vascular plant diversity, and associated animal diversity. We
 combined these metrics into a global Priority Sampling Index (PSI) to
 highlight ways to improve ITRDB representativity. Results: Our refined
 dataset provides access to a network of &gt;52 million growth data
 points worldwide. We found, however, that the database is dominated by
 trees from forests with low diversity, in semi-arid climates, coniferous
 species, and in western North America. Conifers represented 81% of the
 ITRDB and even in well sampled areas, broadleaves were poorly represented.
 Our PSI stressed the need to increase the database diversity in terms of
 broadleaf species and identified poorly represented regions that require
 scientific attention. Great gains will be made by increasing research and
 data sharing in African, Asian, and South American forests. Main
 conclusions: The extensive data and coverage of the ITRDB shows great
 promise to address macroecological questions. To achieve this, however, we
 have to overcome the significant gaps in the representativity of the
 ITRDB. A strategic and organized group effort is required, and we hope the
 tools and data provided here can guide the efforts to improve this
 invaluable database.
description: Appendix S1: Corrected
 and harmonized datasetContent: - Cleaned
 datasets - Conflictive dataset - Duplicated (removed) datasets - Sampling
 coordinates - Error correction log - .rwl files
 metadataAppendix
 S1.zipITRDB-RscriptR code used for analysis and PSI generation
DOI: 10.15468/dl.cwjdss
title: Occurrence Download

description: A dataset containing 5120 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CollectionKey is f707aa14-d87b-4fec-a081-28f3e4ec6a6f",
 "TaxonKey is one of (Phyllostomidae)"
 ]
}

 The dataset includes 5120 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000421-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.f2d1q
title: Data from: Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle

description: The domestication of taurine cattle initiated ~10 000 years ago in the
 Near East from a wild aurochs (Bos primigenius) population followed by
 their dispersal through migration of agriculturalists to Europe. Although
 gene flow from wild aurochs still present at the time of this early
 dispersion is still debated, some of the extant primitive cattle
 populations are believed to possess the aurochs-like primitive features.
 In this study, we use genome-wide single nucleotide polymorphisms to
 assess relationship, admixture patterns and demographic history of an
 ancient aurochs sample and European cattle populations, several of which
 have primitive features and are suitable for extensive management. The
 principal component analysis, the model-based clustering and a
 distance-based network analysis support previous works suggesting
 different histories for north-western and southern European cattle.
 Population admixture analysis indicates a zebu gene flow in the Balkan and
 Italian Podolic cattle populations. Our analysis supports the previous
 report of gene flow between British and Irish primitive cattle populations
 and local aurochs. In addition, we show evidence of aurochs gene flow in
 the Iberian cattle populations indicating wide geographical distribution
 of the aurochs. Runs of homozygosity (ROH) reveal that demographic
 processes like genetic isolation and breed formation have contributed to
 genomic variations of European cattle populations. The ROH also indicate
 recent inbreeding in southern European cattle populations. We conclude
 that in addition to factors such as ancient human migrations, isolation by
 distance and cross-breeding, gene flow between domestic and wild-cattle
 populations also has shaped genomic composition of European cattle
 populations.
description: SNP genotypes and sample
 information for 144 cattle from various primitive European cattle
 breedsThis file contains the
 information for 777,962 markers genotyped in 143 samples using the
 Illumina BovineHD BeadChip. The vcf file contains the aurochs genotypes,
 which corresponds to SNP positions in Illumina BovineHD
 Beadchip.PrimitiveCattleGenotypes.zip
DOI: 10.5061/dryad.6tg35t6
title: Data from: Selection signatures underlying dramatic male inflorescence transformation during modern hybrid maize breeding

description: Inflorescence capacity plays a crucial role in reproductive fitness in
 plants, and in production of hybrid crops. Maize is a monoecious species
 bearing separate male and female flowers (tassel and ear, respectively).
 The switch from open-pollinated populations of maize to hybrid-based
 breeding schemes in the early 20th century was accompanied by a dramatic
 reduction in tassel size, and the trend has continued with modern breeding
 over the recent decades. The goal of this study was to identify selection
 signatures in genes that may underlie this dramatic transformation. Using
 a population of 942 diverse inbred maize accessions and a nested
 association mapping population comprised of three 200-line biparental
 populations, we measured 15 tassel morphological characteristics by manual
 and image-based methods. Genome-wide association studies identified 242
 single nucleotide polymorphisms significantly associated with measured
 traits. We compared 41 unselected lines from the Iowa Stiff Stalk
 Synthetic (BSSS) population to 21 highly selected lines developed by
 modern commercial breeding programs and show that tassel size and weight
 were reduced significantly. We assayed genetic differences between the two
 groups using selection statistics XP-EHH, XP-CLR, and FST. All three
 selection statistics show evidence of selection at genomic regions
 associated with tassel morphology relative to genome-wide null
 distributions. These results support the tremendous effect, both
 phenotypic and genotypic, that selection has had on maize male
 inflorescence morphology.
description: widiv_942g_899784SNPs_imputed_filteredGenos_noRTA_AGPv4.hmp.txt.zipImputed data of 899,784 SNPs generated from RNA-Seq reads of 942 inbred lines. SNPs were called from mapping to the version 4 maize B73 (AGPv4) reference sequence. Imputation was done using fastPHASE v1.4.0 (Scheet and Stephens, 2006).
DOI: 10.5061/dryad.7k82t
title: Data from: How to find home backwards? Locomotion and inter-leg coordination during rearward walking of Cataglyphis fortis desert ants

description: For insects, flexibility in the performance of terrestrial locomotion is a
 vital part of facing the challenges of their often unpredictable
 environment. Arthropods such as scorpions and crustaceans can switch
 readily from forward to backward locomotion, but in insects this behaviour
 seems to be less common and, therefore, is only poorly understood. Here we
 present an example of spontaneous and persistent backward walking in
 Cataglyphis desert ants that allows us to investigate rearward locomotion
 within a natural context. When ants find a food item that is too large to
 be lifted up and to be carried in a normal forward-faced orientation, they
 will drag the load walking backwards to their home nest. A detailed
 examination of this behaviour reveals a surprising flexibility of the
 locomotor output. Compared with forward walks with regular tripod
 coordination, no main coordination pattern can be assigned to rearward
 walks. However, we often observed leg-pair-specific stepping patterns. The
 front legs frequently step with small stride lengths, while the middle and
 the hind legs are characterized by less numerous but larger strides. But
 still, these specializations show no rigidly fixed leg coupling, nor are
 they strictly embedded within a temporal context; therefore, they do not
 result in a repetitive coordination pattern. The individual legs act as
 separate units, most likely to better maintain stability during backward
 dragging.
description: supplementary video V1
 (backward walking)Shown is an ant in
 backward locomotion dragging a large food item. Note that the walking
 pattern is irregular, without any tripod coordination.supplementary video V2
 (forward walking)Shown is an ant walking
 in tripod fashion during forward locomotion. Note that three legs are
 coupled and are swinging in unison, while the other three legs remain on
 the ground.supplementary video V3
 (forward pulling)Ants prefer to walk in
 forward-faced orientation, as long as the shape and weight of a food item
 makes this possible. Shown here is an example of an ant that has a food
 item that is too light-weight for backward dragging and the ant pushes the
 item forwards towards its home nest.supplementary video V4
 (backward tripod-like coordination)Shown is an ant in
 backward locomotion. Generally, a detailed analysis of the ants’ inter-leg
 coordination revealed an irregular locomotion during backward walking.
 However, in this video we find the tendency that the legs of one tripod
 group are swinging more or less simultaneously. This indicates that
 backward tripod coordination is per se possible.
DOI: 10.5061/dryad.kb79121
title: Data from: A high-content imaging approach to profile C. elegans embryonic development

description: The C. elegans embryo is an important model for analyzing mechanisms of
 cell fate specification and tissue morphogenesis. Sophisticated lineaging
 approaches for analyzing embryogenesis have been developed but are
 labor-intensive and do not naturally integrate morphogenetic readouts. To
 enable the rapid classification of developmental phenotypes, we developed
 a high-content method that employs two custom strains: a Germ Layer strain
 expressing nuclear markers in the ectoderm, mesoderm and endoderm/pharynx,
 and a Morphogenesis strain expressing markers labeling epidermal cell
 junctions and the neuronal cell surface. We describe a procedure that
 allows simultaneous live imaging of development in 80-100 embryos and
 provide a custom program that generates cropped, oriented image stacks of
 individual embryos to facilitate analysis. We demonstrate the utility of
 our method by perturbing 40 previously characterized developmental genes
 in variants of the two strains containing RNAi-sensitizing mutations. The
 resulting datasets yielded distinct, reproducible signature phenotypes for
 a broad spectrum of genes involved in cell fate specification and
 morphogenesis. Our analysis additionally provides new in vivo evidence for
 MBK-2 function in mesoderm fate specification and LET-381 function in
 elongation.
description: README_movie_filescontrol_EMBD0000_GLS_longcontrol_EMBD0000_MS_longaph-1_EMBD0022_GLS-1aph-1_EMBD0022_MSapl-1_EMBD0082_GLSapl-1_EMBD0082_MSaps-1_EMBD0013_GLSaps-1_EMBD0013_MSarx-1_EMBD0006_GLS-2arx-1_EMBD0006_MSarx-3_EMBD0055_GLS-2arx-3_EMBD0055_MSast-1_EMBD0074_GLSast-1_EMBD0074_MSceh-43_EMBD0018_GLSceh-43_EMBD0018_MSdie-1_EMBD0009_GLSdie-1_EMBD0009_MSdsh-2_EMBD0038_GLSdsh-2_EMBD0038_MSeff-1_EMBD0042_GLSeff-1_EMBD0042_MSelt-1_EMBD0016_GLSelt-1_EMBD0016_MSemb-9_EMBD0062_GLSemb-9_EMBD0062_MSgex-2_EMBD0005_GLSgex-2_EMBD0005_MSgrh-1_EMBD0012_GLSgrh-1_EMBD0012_MShch-1_EMBD0041_GLShch-1_EMBD0041_MShmg-3_EMBD0003_GLShmg-3_EMBD0003_MShmr-1_EMBD0057_GLShmr-1_EMBD0057_MSlag-1_EMBD0068_GLSlag-1_EMBD0068_MSlam-3_EMBD0014_GLSlam-3_EMBD0014_MSlet-19_EMBD0004_GLSlet-19_EMBD0004_MSlet-381_EMBD0015_GLSlet-381_EMBD0015_MSlet-4_EMBD0026_GLSlet-4_EMBD0026_MSlet-413_EMBD0054_GLSlet-413_EMBD0054_MSlet-502_EMBD0007_GLSlet-502_EMBD0007_MSlin-26_EMBD0052_GLSlin-26_EMBD0052_MSlit-1_EMBD0387_GLSlit-1_EMBD0387_MSmbk-2_EMBD0077_GLSmbk-2_EMBD0077_MSmes-1_EMBD0043_GLSmes-1_EMBD0043_MSmex-3_EMBD0063_GLSmex-3_EMBD0063_MSmom-2_EMBD0386_GLSmom-2_EMBD0386_MSpal-1_EMBD0053_GLSpal-1_EMBD0053_MSpha-1_EMBD0025_GLSpha-1_EMBD0025_MSpha-4_EMBD0002_GLSpha-4_EMBD0002_MSplrg-1_EMBD0076_GLSplrg-1_EMBD0076_MSpop-1_EMBD0388_GLSpop-1_EMBD0388_MSpxn-2_EMBD0039_GLSpxn-2_EMBD0039_MSsem-4_EMBD0080_GLSsem-4_EMBD0080_MSvab-1_EMBD0027_GLSvab-1_EMBD0027_MSvab-19_EMBD0029_GLSvab-19_EMBD0029_MSwrm-1_EMBD0385_GLSwrm-1_EMBD0385_MS
DOI: 10.15468/dl.zd5kvg
title: Occurrence Download

description: A dataset containing 10759 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dichaea"
 ]
}

 The dataset includes 10759 records from 351 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000420-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.