cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4kh67
title: Data from: The role of cis regulatory evolution in maize domestication

description: Gene expression differences between divergent lineages caused by
 modification of cis regulatory elements are thought to be important in
 evolution. We assayed genome-wide cis and trans regulatory differences
 between maize and its wild progenitor, teosinte, using deep RNA sequencing
 in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and
 stem). Pervasive regulatory variation was observed with approximately 70%
 of ~17,000 genes showing evidence of regulatory divergence between maize
 and teosinte. However, many fewer genes (1,079 genes) show consistent cis
 differences with all sampled maize and teosinte lines. For ~70% of these
 1,079 genes, the cis differences are specific to a single tissue. The
 number of genes with cis regulatory differences is greatest for ear
 tissue, which underwent a drastic transformation in form during
 domestication. As expected from the domestication bottleneck, maize
 possesses less cis regulatory variation than teosinte with this deficit
 greatest for genes showing maize-teosinte cis regulatory divergence,
 suggesting selection on cis regulatory differences during domestication.
 Consistent with selection on cis regulatory elements, genes with cis
 effects correlated strongly with genes under positive selection during
 maize domestication and improvement, while genes with trans regulatory
 effects did not. We observed a directional bias such that genes with cis
 differences showed higher expression of the maize allele more often than
 the teosinte allele, suggesting domestication favored up-regulation of
 gene expression. Finally, this work documents the cis and trans regulatory
 changes between maize and teosinte in over 17,000 genes for three tissues.
description: SupplementalDataset1Supplemental Dataset 1: Gene level information for the three tissues including start/stop, chromosome, interpro descriptions, rice and Arabidopsis homologs, selection score from Hufford 2012, depth at segregating sites, binomial and Fisher's exact test p-values, and regulatory category.SupplementalDataset2Supplemental Dataset 2: Gene level counts for the three experimental tissues for each individual maize x teosinte comparison. Data includes depth at segregating sites, number of SNPs, log2 maize:teosinte ratios, binomial test p-values, and amount of sequence obtained.
DOI: 10.5061/dryad.b2t22
title: Data from: Visual receptive field properties of neurons in the mouse lateral geniculate nucleus

description: The lateral geniculate nucleus (LGN) is increasingly regarded as a
 “smart-gating” operator for processing visual information. Therefore,
 characterizing the response properties of LGN neurons will enable us to
 better understand how neurons encode and transfer visual signals. Efforts
 have been devoted to study its anatomical and functional features, and
 recent advances have highlighted the existence in rodents of complex
 features such as direction/orientation selectivity. However, unlike
 well-researched higher-order mammals such as primates, the full array of
 response characteristics vis-à-vis its morphological features have
 remained relatively unexplored in the mouse LGN. To address the issue, we
 recorded from mouse LGN neurons using multisite-electrode-arrays (MEAs)
 and analysed their discharge patterns in relation to their location under
 a series of visual stimulation paradigms. Several response properties
 paralleled results from earlier studies in the field and these include
 centre-surround organization, size of receptive field, spontaneous firing
 rate and linearity of spatial summation. However, our results also
 revealed “high-pass” and “low-pass” features in the temporal frequency
 tuning of some cells, and greater average contrast gain than reported by
 earlier studies. In addition, a small proportion of cells had
 direction/orientation selectivity. Both “high-pass” and “low-pass” cells,
 as well as direction and orientation selective cells, were found only in
 small numbers, supporting the notion that these properties emerge in the
 cortex. ON- and OFF-cells showed distinct contrast sensitivity and
 temporal frequency tuning properties, suggesting parallel projections from
 the retina. Incorporating a novel histological technique, we created a 3-D
 LGN volume model explicitly capturing the morphological features of mouse
 LGN and localising individual cells into anterior/middle/posterior LGN.
 Based on this categorization, we show that the ON/OFF, DS/OS and linear
 response properties are not regionally restricted. Our study confirms
 earlier findings of spatial pattern selectivity in the LGN, and builds on
 it to demonstrate that relatively elaborate features are computed early in
 the visual pathway.
description: cellsA .mat (MATLAB) file
 containing a database of electrophysiological results and recordings
 (spike times). Additional information is provided in the README
 file.samplePlotsSample MATLAB code for generating figures from Tang et al 2015, Visual receptive field properties of neurons in the mouse dorsal lateral geniculate nucleus, PLoS One.
DOI: 10.5061/dryad.6630k
title: Data from: Integrating transcriptional, metabolomic, and physiological responses to drought stress and recovery in switchgrass (Panicum virgatum L.)

description: Background: In light of the changes in precipitation and soil water
 availability expected with climate change, understanding the mechanisms
 underlying plant responses to water deficit is essential. Toward that end
 we have conducted an integrative analysis of responses to drought stress
 in the perennial C4 grass and biofuel crop, Panicum virgatum
 (switchgrass). Responses to soil drying and re-watering were measured at
 transcriptional, physiological, and metabolomic levels. To assess the
 interaction of soil moisture with diel light:dark cycles, we profiled gene
 expression in drought and control treatments under pre-dawn and mid-day
 conditions. Results: Soil drying resulted in reduced leaf water potential,
 gas exchange, and chlorophyll fluorescence along with differential
 expression of a large fraction of the transcriptome (37%). Many
 transcripts responded differently depending on time of day (e.g.
 up-regulation pre-dawn and down-regulation mid-day). Genes associated with
 C4 photosynthesis were down-regulated during drought, while C4 metabolic
 intermediates accumulated. Rapid changes in gene expression were observed
 during recovery from drought, along with increased water use efficiency
 and chlorophyll fluorescence. Conclusions: Our findings demonstrate that
 drought responsive gene expression depends strongly on time of day and
 that gene expression is extensively modified during the first few hours of
 drought recovery. Analysis of covariation in gene expression, metabolite
 abundance, and physiology among plants revealed non-linear relationships
 that suggest critical thresholds in drought stress responses. Future
 studies may benefit from evaluating these thresholds among diverse
 accessions of switchgrass and other C4 grasses.
description: Annotated FASTA file of
 custom Panicum virgatum (Alamo AP13) transcriptome
 assemblyA custom transcriptome
 assembly produced from publicly available EST data from accession Alamo
 AP13 (454 data from NCBI’s Sequence Read Archive: accessions
 SRR187765-SRR187775; Sanger sequences from cDNA libraries CFNU, CFNT, and
 EXTA; Zhang et al., 2013). Reads were quality filtered, screened for
 adaptor and vector contamination, and assembled in Roche De Novo Assembler
 v2.6 with the ‘-cdna’ option. This FASTA file has been compressed using
 the GZIP utility.AlamoAP13_annotated_transcriptome.fasta.gzAlamoAP13_transcriptome_annotationsHomology-based annotations for the custom P. virgatum Alamo AP13 transcriptome. A tab-delimited text file. Column IDs: Seq=sequence identifier; Isogroup=cluster of transcripts thought to originate from the same gene; Len=length in base pairs; Match=accession number of best match; Gene=name of the best match; GO=Gene Ontology terms associated with the best match.
DOI: 10.5061/dryad.dh62b
title: Data from: Radar wind profilers and avian migration - a qualitative and quantitative assessment verified by thermal imaging and moon watching

description: 1. Radars of various types have been used in ornithological research for
 about 70 years. However, the potential of radar wind profiler (RWP) as a
 tool for biological purposes remains poorly understood. The aim of this
 study is to assess the suitability of RWP for ornithological research
 questions. 2. A 1290 MHz RWP at the southeastern coast of the Bay of
 Biscay has been known to exhibit seasonally occurring nocturnal signals
 attributed to migrating birds. As a first step to verify the origin of
 these seasonal patterns, historical radar data from 2010-2012 were
 analysed, and both bird patterns and temporal occurrence were identified
 in RWP data at different levels of the signal processing. A
 thermal-imaging (TI) camera in conjunction with moon watching was used as
 verification systems at the radar site to confirm the ornithological
 origin of the radar echoes. The simultaneous data on spring migration
 served as a basis for the identification of biological signatures
 (qualitative parameters) on time series level (raw data) and to derive
 quantitative migration parameters (flight altitude, migration traffic
 rates) thereof. Finally the quantitative measurements of the TI camera and
 the radar were compared considering meteorological conditions. 3. The
 approach allowed identifying reproducible criteria based on time series to
 calculate migration traffic rates and altitudinal flight distribution.
 General flight directions were only available in the final wind data. In
 clear weather conditions the calibration methods coincided well with the
 wind profiler data. 4. Findings show that wind profiler raw data offers
 reliable information on migration intensity, flight altitudes and flight
 directions in a variety of meteorological conditions. The method presented
 can be applied as a complement to present efforts to use weather radars
 for large-scale bird monitoring. Furthermore it is also interesting for
 the meteorological community to refine signal-processing methods.
description: TimeSeriesPlots of analysed time series data for each 4-hours interval in March 2015 from the Punta Galea radar wind profiler.
DOI: 10.5061/dryad.s8v80
title: Data from: Hidden histories of gene flow in highland birds revealed with genomic markers

description: Genomic studies are revealing that divergence and speciation are marked by
 gene flow, but it is not clear whether gene flow has played a prominent
 role during the generation of biodiversity in species-rich regions of the
 world where vicariance is assumed to be the principal mode by which new
 species form. We revisit a well-studied organismal system in the Mexican
 Highlands, Aphelocoma jays, to test for gene flow among Mexican sierras.
 Prior results from mitochondrial DNA (mtDNA) largely conformed to the
 standard model of allopatric divergence, although there was also evidence
 for more obscure histories of gene flow in a small sample of nuclear
 markers. We tested for these ‘hidden histories’ using genomic markers
 known as ultraconserved elements (UCEs) in concert with phylogenies,
 clustering algorithms and newer introgression tests specifically designed
 to detect ancient gene flow (e.g. ABBA/BABA tests). Results based on 4303
 UCE loci and 2500 informative SNPs are consistent with varying degrees of
 gene flow among highland areas. In some cases, gene flow has been
 extensive and recent (although perhaps not ongoing today), whereas in
 other cases there is only a trace signature of ancient gene flow among
 species that diverged as long as 5 million years ago. These results show
 how a species complex thought to be a model for vicariance can reveal a
 more reticulate history when a broader portion of the genome is queried.
 As more organisms are studied with genomic data, we predict that
 speciation-with-bouts-of-gene-flow will turn out to be a common mode of
 speciation.
description: Structure Input
 FileData matrix for
 Structure runsSTRUCTURE_input.txtSNAPP Input FileInput file for SNAPP species tree runs in BEASTSNAPP_input.xmlSNP_callsVarious files associated with calling SNPs from UCE loci for use with SNAPP and StructureUCE Data MatrixConcatenated UCE data matrix for phylogenetic analysisS_File_2_UCE_incomplete_matrix_alignment_labeled.phylipmtDNA alignmentAlignment of 13 mtDNA protein coding gene for phylogenetic analysisS_File_3_mtDNA_prot_cod_reg_alignment_labeled.phylipmtDNA partitionsPartition file for mtDNA alignmentS_File_4_mtDNA_partitions_for_RAxML.txtDNA Data Statistics TableExtended table with statistics on sequenced DNA data for individual specimensS1_Statistics_table.xlsxScripts for SNP CallingVarious custom scripts used to call SNPs for Structure and SNAPPScripts.zip
DOI: 10.5061/dryad.1gk2p
title: Data from: Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic–pituitary–gonadal (HPG) axis

description: The hypothalamic-pituitary-gonadal (HPG) axis is a key biological system
 required for reproduction and associated sexual behaviors to occur. In the
 avian reproductive model of the rock dove (Columba livia), we
 characterized the transcript community of each tissue of the HPG axis in
 both sexes, thereby significantly expanding our mechanistic insight into
 HPG activity. We report greater sex-biased differential expression in the
 pituitary as compared to the hypothalamus, with multiple genes more highly
 expressed in the male pituitary being related to secretory function, and
 multiple genes more highly expressed in the female pituitary being related
 to reproduction, growth, and development. We report tissue-specific and
 sex-biased expression in genes commonly investigated when studying
 reproduction, highlighting the need for sex parity in future studies. In
 addition, we uncover new targets of investigation in both sexes, which
 could potentially change our understanding of HPG function.
description: RockDove.HPG.v1.0.3.gff3Annotation file for assemblyRockDove.HPG.v1.0.3.fastaTranscriptome assembly file
DOI: 10.5061/dryad.vb131
title: Data from: First insights into the transcriptome and development of new genomic tools of a widespread circum-Mediterranean tree species, Pinus halepensis Mill.

description: Pinus halepensis is a relevant conifer species for studying adaptive
 responses to drought and fire regimes in the Mediterranean region.
 Deciphering the molecular basis of Aleppo pine to the Mediterranean
 environment is therefore needed. In this study we performed Illumina
 next-generation sequencing of two phenotypically divergent Pinus
 halepensis accessions with the aims of i) characterizing the transcriptome
 through Illumina RNA-Seq of two accessions, phenotypically divergent for
 adaptive traits link to fire adaptation and drought, ii) performing a
 functional annotation of the assembled transcriptome, iii) identifying
 genes with accelerated evolutionary rates, iv) studying the expression
 levels of the annotated genes, and v) developing gene-based markers for
 population genomic and association genetic studies. The assembled
 transcriptome consisted in 48,629 contigs and covered about 54.6 Mbp. The
 comparison of P. halepensis transcripts to Picea sitchensis protein-coding
 sequences resulted in the detection of 34,014 SNPs across species, with a
 Ka/Ks average value of 0.216, suggesting that the majority of the
 assembled genes are under negative selection. Assembled genes showed an
 over-representation in expression of genes involved in protein synthesis.
 Several genes were differentially expressed across the two pine accessions
 with contrasted phenotypes, including glutathione s-transferase, the
 cellulose synthase and the cobra-like protein . A large number of new
 markers (8,248 SSRs and 28,236 SNPs) has been identified which should
 facilitate future population genomics and association genetics in this
 species. Our results showed that Illumina next-generation sequencing is a
 valuable technology to obtain an extensive overview on whole
 transcriptomes of non-model species with large genomes.
description: Pinus halepensis GO
 annotationAssembled sequences and
 singletons subjected to BLAST2GO similarity searches and annotated with
 Gene Ontology (GO).Phalepensis_GO_annotation.xlsxPinus halepensis__KEGG_annotationKyoto Encyclopaedia of Genes and Genomes (KEGG) pathway annotations of the assembled transcripts.Pinus halepensis transcriptome sequenceAssembled sequence of Pinus halepensis transcriptomePinus halepensis_transcriptome.fasta
DOI: 10.5061/dryad.0582b8b
title: Data from: Possible causes of divergent population trends in sympatric African herbivores

description: Sympatric herbivores experience similar environmental conditions but can
 vary in their population trends. Identifying factors causing these
 differences could assist conservation efforts aimed at maintaining fully
 functional ecosystems. From 1996 – 2013, tsessebe and wildebeest
 populations in the Okavango Delta, Botswana, declined by 73% and 90%,
 respectively, whereas zebra populations remained stable. These sympatric,
 medium sized herbivores are exposed to similar natural and anthropogenic
 pressures, but apparently differ in their responses to those pressures. To
 identify factors that could cause these differences, we fitted GPS-enabled
 collars to six zebra, eight tsessebe and seven wildebeest in the Moremi
 Game Reserve, Botswana. We calculated utilisation distributions (UDs) from
 GPS data, and used 95% isopleths to compare seasonal home range size
 between species. We calculated utilisation intensity (UI) from the UDs and
 generated spatial layers representing resources and disturbances, and then
 used model averaging to identify factors affecting UI for each species. We
 calculated second and third order habitat selection ratios to determine
 whether species were habitat specialists or generalists. Zebra occupied
 larger home ranges than tsessebe and wildebeest, showed weaker responses
 to spatial variables and displayed no third order habitat selection; zebra
 social systems are also more fluid, allowing for information exchange
 between stable harems. Herbivore species that are sedentary, occupy small
 home ranges, are habitat specialists and exist in relatively isolated
 groups are likely to be less resistant and resilient to the rapid pace of
 environmental change forecast by climate change scenarios. Resources
 contained within existing protected areas are unlikely to maintain
 populations of such species at sufficiently high levels, potentially
 leading to functional extinction. Special precautions may be needed to
 ensure that such species can persist in the wild, such as buffer zones
 around existing protected areas, which would allow greater potential for
 adaptive movement should current environmental conditions change.
description: Population trends
 dataData on home range size,
 habitat selection and factors affecting spatial distribution of zebra,
 tsessebe and blue wildebeest in the Okavango Delta
DOI: 10.5061/dryad.ps837
title: Data from: Massive sequencing of Ulmus minor's transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease

description: Elms, especially Ulmus minor and Ulmus americana, are carrying out a hard
 battle against Dutch elm disease (DED). This vascular wilt disease, caused
 by Ophiostoma ulmi and O. novo-ulmi, appeared in the twentieth century and
 killed millions of elms across North America and Europe. Elm breeding and
 conservation programmes have identified a reduced number of DED tolerant
 genotypes. In this study, three U. minor genotypes with contrasted levels
 of tolerance to DED were exposed to several biotic and abiotic stresses in
 order to (i) obtain a de novo assembled transcriptome of U. minor using
 454 pyrosequencing, (ii) perform a functional annotation of the assembled
 transcriptome, (iii) identify genes potentially involved in the molecular
 response to environmental stress, and (iv) develop gene-based markers to
 support breeding programmes. A total of 58,429 putative unigenes were
 identified after assembly and filtering of the transcriptome. 32,152 of
 these unigenes showed homology with proteins identified in the genome from
 the most common plant model species. Well-known family proteins and
 transcription factors involved in abiotic, biotic or both stresses were
 identified after functional annotation. A total of 30,693 polymorphisms
 were identified in 7,125 isotigs, a large number of them corresponding to
 SNPs (27,359). In a subset randomly selected for validation, 87 % of the
 SNPs were confirmed. The material generated may be valuable for future
 Ulmus gene expression, population genomics and association genetics
 studies, especially taking into account the scarce molecular information
 available for this genus and the great impact that DED has on elm
 populations.
description: Ulmus_minor_INFO_unigenesUnigenes description. This document shows the sequence lenght; protein name; information from the best blast hit; GO terms associated to the sequence; Enzyme Codes (ECs); Domains; Sequence assiated to abiotic; biotic or both stimulus; Sequences with SNPs.Ulmus_minor_INFO_redundant_sequencesRedundant sequences description. This document shows the sequence lenght; protein name; information from the best blast hit; GO terms associated to the sequence; Enzyme Codes (ECs); Domains; Sequence assiated to abiotic; biotic or both stimulus; Sequences with SNPs.Ulmus_minor_KEEG_annotation_unigenesUnigenes associated to different KEEG pathwaysUlmus_minor_GO_annotation_unigenesGO annotation of UnigenesUlmus_minor_POLYMORPHISM_identificationIdentification and location of SNPs and other polymorphismsUlmus_minor_transcriptomeSequences from full transcriptoma in Fasta formatFungus_transcripts181 Unique transcripts that show homology with genome of inoculated organisms.