cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nn952
title: Data from: The early spread and epidemic ignition of HIV-1 in human populations

description: Thirty years after the discovery of HIV-1, the early transmission,
 dissemination and establishment of the virus in human populations remain
 unclear. Using statistical approaches applied to HIV-1 sequence data from
 central Africa, we show that from the 1920s Kinshasa was the focus of
 early transmission and the source of pre-1960 pandemic viruses elsewhere.
 Location and dating estimates were validated using the earliest HIV-1
 archival sample, also from Kinshasa. The epidemic histories of HIV-1 group
 M and non-pandemic group O were similar until ~1960, after which group M
 underwent an epidemiological transition and outpaced regional population
 growth. Our results reconstruct the early dynamics of HIV-1 and emphasize
 the role of social changes and transport networks in the establishment of
 this virus in human populations.
description: Preliminary
 AnalysisContains (1) BEAST XML
 input file, (2) empirical tree distribution (1,000 trees) (GTR+gamma
 substitution model, uncorrelated relaxed clock model, skygrid tree prior),
 and (3) nexus format sequence alignment.Sequence data details
 and alignments for data sets A to DContains (1) table with
 accession numbers, isolate names, sampling years, country/location of
 sampling and (2) nexus format sequence alignments.Sequence data details and
 alignments.zipPhylogeographic models
 and empirical tree distributions for data sets A to DContains (1) the BEAST
 XML input file used to generate Figure 1; (2) BEAST XML files used to
 generate the phylogeographic analyses with an asymmetric diffusion model
 in Tables S2-S5; and (3) empirical tree distributions (2,000 trees)
 (GTR+gamma substitution model, uncorrelated relaxed clock model, skygrid
 tree prior).Phylogeographic models and
 empirical tree distributions.zipExponential-logistic
 coalescent model, robust counting and randomisation
 procedureContains (1) the BEAST
 XML input file for the exponential-logistic coalescent model used to
 estimate the epidemiological transition time, (2) the BEAST XML input file
 for the robust counting analysis (Fig. 3 and Figs. S5-S6), and (3) the
 BEAST XML input file corresponding to the randomisation procedure shown in
 Fig. S4.Exponential-logistic
 demographic mode, robust counting and randomisation
 procedure.zip
DOI: 10.34740/kaggle/dsv/14631092
title: Berita UII
DOI: 10.5061/dryad.tk2fn
title: Data from: Comparative transcriptomics uncovers alternative splicing changes and signatures of selection from maize improvement

description: Background: Alternative splicing (AS) is an important regulatory mechanism
 that greatly contributes to eukaryotic transcriptome diversity. A
 substantial amount of evidence has demonstrated that AS complexity is
 relevant to eukaryotic evolution, development, adaptation, and complexity.
 In this study, six teosinte and ten maize transcriptomes were sequenced to
 analyze AS changes and signatures of selection in maize domestication and
 improvement. Results In maize and teosinte, 13,593 highly conserved genes,
 including 12,030 multiexonic genes, were detected. By identifying AS
 isoforms from mutliexonic genes, we found that AS types were not
 significantly different between maize and teosinte. In addition, the two
 main AS types (intron retention and alternative acceptor) contributed to
 more than 60% of the AS events in the two species, but the average unique
 AS events per each alternatively spliced gene in maize (4.12) was higher
 than that in teosinte (2.26). Moreover, 94 genes generating 98 retained
 introns with transposable element (TE) sequences were detected in maize,
 which is far more than 9 retained introns with TEs detected in teosinte.
 This indicates that TE insertion might be an important mechanism for
 intron retention in maize. Additionally, the AS levels of 3864 genes were
 significantly different between maize and teosinte. Of these, 151 AS
 level-altered genes that are involved in transcriptional regulation and in
 stress responses are located in regions that have been targets of
 selection during maize improvement. These genes were inferred to be
 putatively improved genes. Conclusions We suggest that both maize and
 teosinte share similar AS mechanisms, but more genes have increased AS
 complexity during domestication from teosinte to maize. Importantly, a
 subset of AS level-increased genes that encode transcription factors and
 stress-responsive proteins may have been selected during maize
 improvement.
description: SNPs in HapMap
 formatA HapMap format file
 containing SNPs that were used for phylogenetic
 analysis.maize-teosinte.hap.txtAlignment file used for phylogenetic tree analysisA phylip sequential format file that was used to reconstruct NJ tree.alignment.sequential.txtNeighbor-joining tree between maize and teosinteThe phylogenetic analysis was performed using the neighbor-joining method with 1000 bootstrap replicates in the PHYLIP packagemaize-teosinte.outtree
DOI: 10.5061/dryad.0mq69
title: Data from: Long-term differences in extinction risk among the seven forms of rarity

description: Rarity is widely used to predict the vulnerability of species to
 extinction. Species can be rare in markedly different ways, but the
 relative impacts of these different forms of rarity on extinction risk are
 poorly known and cannot be determined through observations of species that
 are not yet extinct. The fossil record provides a valuable archive with
 which we can directly determine which aspects of rarity lead to the
 greatest risk. Previous paleontological analyses confirm that rarity is
 associated with extinction risk, but the relative contributions of
 different types of rarity to extinction risk remain unknown because their
 impacts have never been examined simultaneously. Here, we analyze a global
 database of fossil marine animals spanning the past 500 million years,
 examining differential extinction with respect to multiple rarity types
 within each geological stage. We observe systematic differences in
 extinction risk over time among marine genera classified according to
 their rarity. Geographic range played a primary role in determining
 extinction, and habitat breadth a secondary role, whereas local abundance
 had little effect. These results suggest that current reductions in
 geographic range size will lead to pronounced increases in long-term
 extinction risk even if local populations are relatively large at present.
description: PaleoDB raw occurrence
 data downloaded 25-09-2010The data used for our
 study were downloaded from the Paleobiology Database (PaleoDB) on 25
 September 2010. The download included all occurrences entered by the
 Marine Invertebrate Working Group, excluding vertebrates and genera listed
 in quotation marks or qualified as "?", "cf.", or
 "aff." were excluded from the subsequent analysis. The following
 data associated with each occurrence were also downloaded: paleolatitude,
 paleolongitude, paleoenvironment, primary lithology, and taxon abundance.
 Please see the PaleoDB (http://http://paleodb.org) for additional details
 regarding data fields.Harnik-et-al-raw-occurrence-data-PaleoDB-download-25-09-2010.csvHarnik et al - Phanerozoic rarity and extinction dataHarnik-et-al-Phanerozoic-rarity-data.csv
DOI: 10.5061/dryad.8182t
title: Data from: The genome sequence and insights into the immunogenetics of the bananaquit (Passeriformes: Coereba flaveola)

description: Avian genomics, especially of non-model species, is in its infancy
 relative to mammalian genomics. Here, we describe the sequencing,
 assembly, and annotation of a new avian genome, that of the bananaquit
 Coereba flaveola (Passeriformes: Thraupidae). We produced ∼30-fold
 coverage of the genome with an assembly size of ca. 1.2 Gb, including
 approximately 16,500 annotated genes. Passerine birds, such as the
 bananaquit, are commonly infected by avian malarial parasites
 (Haemosporida), which presumably drive adaptive evolution of immunogenetic
 loci within the host genome. In the context of our research on the
 distribution of avian Haemosporida, we specifically characterized immune
 loci, including toll-like receptor (TLR) and major histocompatibility
 complex (MHC) genes. Additionally, we identified novel molecular markers
 in the form of single nucleotide polymorphisms (SNPs), both genome-wide
 and within identified immune loci. We discovered nine TLR genes and four
 MHC genes and identified five other TLR- or MHC- associated genes.
 Genome-wide, over 6 million high-quality SNPs were annotated, including
 568 within TLR genes and 102 in MHC genes. This newly described genome and
 immune characterization expands the knowledge base for avian genomics and
 phylogenetics and allows for immune genotyping in the bananaquit,
 providing tools for the investigation of host-parasite coevolution.
description: Bananaquit (Coereba
 flaveola) genome annotationStructural and
 functional annotation (.gff) file for the genes, exons, and CDS from
 bananaquit genome sequencing and assembly (NCBI Bioproject ID:
 PRJNA353240).bananaquit_annotation_genome.gffBananaquit (Coereba flaveola) transcriptsFasta file for the annotated transcripts from bananaquit genome sequencing and assembly (NCBI Bioproject ID: PRJNA353240).soapmaster_merged.gam.min500.all.maker.transcripts.fastaBananaquit (Coereba flaveola) proteinsFasta file for the annotated proteins from bananaquit genome sequencing and assembly (NCBI Bioproject ID: PRJNA353240).soapmaster_merged.gam.min500.all.maker.proteins.fastaBioproject ID: PRJNA353240NCBI Bioproject including sequencing reads, genome assembly, annotated SNPs, and BioSamples.
DOI: 10.5061/dryad.8395f
title: Data from: The origin and evolution of coral species richness in a marine biodiversity hotspot

description: The Coral Triangle region of the Indo-Pacific realm harbors an
 extraordinary number of species, with richness decreasing away from this
 biodiversity hotspot. Despite multiple competing hypotheses, the dynamics
 underlying this regional diversity pattern remain poorly understood. Here
 we use a time-calibrated evolutionary tree of living reef coral species,
 their current geographic ranges, and model-based estimates of regional
 rates of speciation, extinction, and geographic range shifts to show that
 origination rates within the Coral Triangle are lower than in surrounding
 regions, a result inconsistent with the long-standing center of origin
 hypothesis. Furthermore, endemism of coral species in the Coral Triangle
 is low, and the Coral Triangle endemics are older than relatives found
 outside this region. Overall, our model results suggest that the high
 diversity of reef corals in the Coral Triangle is largely due to range
 expansions into this region of species that evolved elsewhere. These
 findings strongly support the notion that geographic range shifts play a
 critical role in generating species diversity gradients. They also show
 that preserving the processes that gave rise to the striking diversity of
 corals in the Coral Triangle requires protecting not just reefs within the
 hotspot, but also those in the surrounding areas.
description: SpeciesList of all scleractinian corals showing reef species, geographic states according to Hughes et al. (2013) and Veron et al. (2009, 2011) (0 = widespread, 1 = endemic to CT, 2 = outside of CT), as well as GenBank and morphological data sources used to reconstruct the phylogeny of Scleractinia (doi:10.1098/rstb.2014.0010) and Acroporidae.RSTBtree1000 posterior trees of Scleractinia based on random resolutions of the supertree (doi:10.1098/rstb.2014.0010); used for GeoSSE analyses.Acroporidae inputBEAST input file used to generate the Acroporidae molecular trees.Acroporidae.xmlAcroporidae trees1000 posterior trees of Acroporidae based on molecular data only; used for GeoSSE analyses.Acroporidae.treGeoSSER code used to fit GeoSSE model using maximum likelihood and Bayesian Markov chain Monte Carlo.patch_diversitreeR code containing patch for the package "diversitree" to use hidden states.
DOI: 10.5061/dryad.h2kh3
title: Data from: Strong trans-Pacific break and local conservation units in the Galapagos shark (Carcharhinus galapagensis) revealed by genome-wide cytonuclear markers

description: The application of genome-wide cytonuclear molecular data to identify
 management and adaptive units at various spatio-temporal levels is
 particularly important for overharvested large predatory organisms, often
 characterized by smaller, localized populations. Despite being “near
 threatened”, current understanding of habitat use and population structure
 of Carcharhinus galapagensis is limited to specific areas within its
 distribution. We evaluated population structure and connectivity across
 the Pacific Ocean using genome-wide Single Nucleotide Polymorphisms (~7200
 SNPs) and mitochondrial Control Region sequences (947bp) for 229
 individuals. Neutral SNPs defined at least two genetically discrete
 geographic groups: an East Tropical Pacific (Mexico, east and west
 Galapagos Islands), and another central-west Pacific (Lord Howe Island,
 Middleton Reef, Norfolk Island, Elizabeth Reef, Kermadec, Hawaii and
 Southern Africa). More fine-grade population structure was suggested using
 outlier SNPs: west Pacific, Hawaii, Mexico, and Galapagos. Consistently,
 mtDNA pairwise ΦST defined three regional stocks: east, central and west
 Pacific. Compared to neutral SNPs (FST=0.023-0.035), mtDNA exhibited more
 divergence (ΦST=0.258-0.539) and high overall genetic diversity (h=0.794
 ±0.014; π=0.004 ±0.000), consistent with the longstanding Eastern Pacific
 Barrier between the east and central-west Pacific. Hawaiian and Southern
 African populations group within the west Pacific cluster. Effective
 population sizes were moderate/high for east/west populations (738 and
 3421, respectively). Insights into the biology, connectivity, genetic
 diversity, and population demographics informs for improved conservation
 of this species, by delineating three to four conservation units across
 their Pacific distribution. Implementing such conservation management may
 be challenging, but is necessary to achieve long-term population
 resilience at basin and regional scales.
description: Report-DWh15-1847_2row_for_dartqc_all_indivOriginal (raw) report from DArTseq in two-row format for 3 individuals of Carcharhinus obscurus and 211 individuals of C. galapagensis from nine locations across the Indo-Pacific (Mexico, east and west Galapagos Islands, Lord Howe Island, Middleton Reef, Norfolk Island, Elizabeth Reef, Kermadec, Hawaii and Southern Africa). The excel sheet contains information of Allele ID, Clone ID, AlleleSequence, SNP Position, CallRate, Homozygous and Heterozygous frequency, and average reproducibility.
DOI: 10.5061/dryad.7h81d
title: Data from: Splicing repression allows the gradual emergence of new Alu-exons in primate evolution

description: Alu elements are retrotransposons that frequently form new exons during
 primate evolution. Here, we assess the interplay of splicing repression by
 hnRNPC and nonsense-mediated mRNA decay (NMD) in the quality control and
 evolution of new Alu-exons. We identify 3100 new Alu-exons and show that
 NMD more efficiently recognises transcripts with Alu-exons compared to
 other exons with premature termination codons. However, some Alu-exons
 escape NMD, especially when an adjacent intron is retained, highlighting
 the importance of concerted repression by splicing and NMD. We show that
 evolutionary progression of 3' splice sites is coupled with longer
 repressive uridine tracts. Once the 3' splice site at ancient
 Alu-exons reaches a stable phase, splicing repression by hnRNPC decreases,
 but the exons generally remain sensitive to NMD. We conclude that
 repressive motifs are strongest next to cryptic exons and that gradual
 weakening of these motifs contributes to the evolutionary emergence of new
 alternative exons.
description: List of exons and DEXseq
 analysis in RNAseq data set E-MTAB-6008.This data set was
 created using cufflinks and DEXseq, using Ensembl GRCh37 version 72 as
 input annotation. For detailled description, see associated publication.
 Columns included are genomic position, Ensembl transcript and exon ID,
 base mean across conditions, and statistical testing by DEXseq. Exon_class
 indicated if the exon is an Alu-exon, a cryptic exon, or not. UCSCoverlap
 and type indicate if the exon is annotated by UCSC, and if it is a
 constitutive or alternative exon. If the exon is not annotated in UCSC,
 it's called a cryptic exon. Stand_alone exons are not predicted by
 cufflinks to overlap with another exon. The table also includes the number
 of junction reads confirming either splice site. In addition, we predicted
 premature stop codons in protein coding genes; for PTC+ exons it includes
 the distance between the PTC and downstream exon-exon junction, the
 following (second) exon-exon junction, the number of downstream exons. The
 last two columns show the ID after merging all discovered Alu-exons with
 UCSC annotated Alu-exons, and the grouping of evolutionary groups shown in
 Figure 5 of the associated publication.supplfile10.tab.gz
DOI: 10.5061/dryad.hf591
title: Data from: Modelled three-dimensional suction accuracy predicts prey capture success in three species of centrarchid fishes

description: Prey capture is critical for survival, and differences in correctly
 positioning and timing a strike (accuracy) are likely related to variation
 in capture success. However, an ability to quantify accuracy under natural
 conditions, particularly for fishes, is lacking. We developed a predictive
 model of suction hydrodynamics and applied it to natural behaviours using
 three-dimensional kinematics of three centrarchid fishes capturing evasive
 and non-evasive prey. A spheroid ingested volume of water (IVW) with
 dimensions predicted by peak gape and ram speed was verified with known
 hydrodynamics for two species. Differences in capture success occurred
 primarily with evasive prey (64–96% success). Micropterus salmoides had
 the greatest ram and gape when capturing evasive prey, resulting in the
 largest and most elongate IVW. Accuracy predicted capture success,
 although other factors may also be important. The lower accuracy
 previously observed in M. salmoides was not replicated, but this is likely
 due to more natural conditions in our study. Additionally, we discuss the
 role of modulation and integrated behaviours in shaping the IVW and
 determining accuracy. With our model, accuracy is a more accessible
 performance measure for suction-feeding fishes, which can be used to
 explore macroevolutionary patterns of prey capture evolution.
description: Raw
 data2D PIV data, 3D
 kinematic data, 3D IVW coordinatesSample video
 1Lepomis macrochirus
 capturing evasive prey (success), 33 frames, recorded at 500
 fpsLmac07
 trial 17f Feeding L.aviSample video
 2Lepomis macrochirus
 capturing evasive prey (success), 33 frames, recorded at 500
 fpsLmac07
 trial 17f Feeding V.aviSample smoothed
 pointsSmoothed data from
 sample video: 1 Prey, 2 upper jaw, 3 lower jaw, 4 predator center of mass
 (digitized points)
DOI: 10.5061/dryad.425rs
title: Data from: Individual-based measurements of light intensity provide new insights into the effects of artificial light at night on daily rhythms of urban-dwelling songbirds

description: 1. The growing interest in the effects of light pollution on daily and
 seasonal cycles of animals has led to a boost of research in recent years.
 In birds, it has been hypothesized that artificial light at night can
 affect daily aspects of behaviour, but one caveat is the lack of knowledge
 about the light intensity that wild animals, such as birds, are exposed to
 during the night. 2. Organisms have naturally evolved daily rhythms to
 adapt to the 24-h cycle of day and night, thus, it is important to
 investigate the potential shifts in daily cycles due to global
 anthropogenic processes such as urbanization. 3. We captured adult male
 European blackbirds (Turdus merula) in one rural forest and two urban
 sites differing in the degree of anthropogenic disturbance. We tagged
 these birds with light loggers and simultaneously recorded changes in
 activity status (active/non-active) through an automated telemetry system.
 We first analysed the relationship between light at night, weather
 conditions and date with daily activity onset and end. We then compared
 activity, light at night exposure and noise levels between weekdays and
 weekends. 4. Onset of daily activity was significantly advanced in both
 urban sites compared to the rural population, while end of daily activity
 did not vary either among sites. Birds exposed to higher amounts of light
 in the late night showed earlier onset of activity in the morning, but
 light at night did not influence end of daily activity. Light exposure at
 night and onset/end of daily activity timing was not different between
 weekdays and weekends, but all noise variables were. A strong seasonal
 effect was detected in both urban and rural populations, such as birds
 tended to be active earlier in the morning and later in the evening
 (relative to civil twilight) in the early breeding season than at later
 stages. 5. Our results point at artificial light at night as a major
 driver of change in timing of daily activity. Future research should focus
 on the costs and benefits of altered daily rhythmicity in birds thriving
 in urban areas.
description: Statistical
 modelsR script used to run all
 statistical models included in the manuscriptmodels.ROnset of activityDataframe for the analyses of the onset of activity datadatlight_on.csvOffset of activityDataframe for the analyses of the offset of activitydatlight_off.csvraw activity