cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4gh6hf5g
title: Data from: Strong selection against hybrids maintains a narrow contact zone between morphologically cryptic lineages in a rainforest lizard

description: Phenotypically cryptic lineages comprise an important yet understudied
 part of biodiversity; in particular, we have much to learn about how these
 lineages are formed and maintained. To better understand the evolutionary
 significance of such lineages, we studied a hybrid zone between two
 morphologically-cryptic phylogeographic lineages in the rainforest lizard,
 Lampropholis coggeri. Analyzing a multilocus genetic dataset through cline
 inference, individual-based methods and population measures of
 disequilibrium and using simulations to explore our genetic results in
 context of theoretical expectations, we inferred the processes maintaining
 this hybrid zone. We find that these lineages meet in a hybrid zone that
 is narrow (~400 m) relative to inferred dispersal rate. Further, the
 hybrid zone exhibits substantial genetic disequilibrium and sharply
 coincident and largely concordant clines. Based on our knowledge about the
 region's biogeography, the species' natural history, and our
 simulation results, we suggest that strong selection against hybrids
 structures this system. As all clines show a relatively narrow range of
 introgression, we posit that this hybrid zone might not yet be in
 equilibrium. Nonetheless, our results clearly show that phylogeographic
 lineages can evolve substantial reproductive isolation without concomitant
 morphological diversification, suggesting that such lineages can
 constitute a significant component of evolutionary diversity.
description: Genotypes for
 Lampropholis coggeriHas genotypes for all 11
 loci assayed for all individuals in this study. Individuals are identified
 by easting & northing and by the population in which they are
 located.lamcoggGenotypes.csvBase script used for simulationsScript written in Python used to do simulations of the hybrid zone. Requires simuPOP.hybridSim.pyTranscriptome for Lampropholis coggeriAssembled transcriptome for Lampropholis coggeri, the Northern lineage. The transcripts are annotated both with respect to (1) the known gene they match (if any) and (2) the UTR, CDS of the gene.lamcoggTransciptome.fa
DOI: 10.5061/dryad.c75sj
title: Data from: Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples

description: DNA metabarcoding is an efficient method for measuring biodiversity, but
 the process of initiating long-term DNA-based monitoring programs, or
 integrating with conventional programs, is only starting. In marine
 ecosystems, plankton surveys using the continuous plankton recorder (CPR)
 have characterised biodiversity along transects covering millions of
 kilometres with time-series spanning decades. We investigated the
 potential for use of metabarcoding in CPR surveys. Samples (n= 53) were
 collected in two Southern Ocean transects and metazoans identified using
 standard microscopic methods and by high-throughput sequencing of a
 cytochrome c oxidase subunit I marker. DNA increased the number of
 metazoan species identified and provided high resolution taxonomy of
 groups problematic in conventional surveys (e.g. larval echinoderms and
 hydrozoans). Metabarcoding also generally produced more detections than
 microscopy, but this sensitivity may make cross-contamination during
 sampling a problem. In some samples, the prevalence of DNA from large
 plankton such as krill masked the presence of smaller species. We
 investigated adding a fixed amount of exogenous DNA to samples as an
 internal control to allow determination of relative plankton biomass.
 Overall, the metabarcoding data represents a substantial shift in
 perspective, making direct integration into current long-term time-series
 challenging. We discuss a number of hurdles that exist for progressing DNA
 metabarcoding from the current snapshot studies to the requirements of a
 long-term monitoring program. Given the power and continually increasing
 efficiency of metabarcoding, it is almost certain this approach will play
 an important role in future plankton monitoring.
description: 1_CPR_DNA_sequencesDNA sequences (merged sequence text files in FASTA format) for each sample as well as various files (mostly .csv format) with information on the identity of samples, taxonomy assigned to OTUs, etc... needed for initial data processing. These files are called in the r code (1) below.2_CPR_Final_DataSummaries including DNA sequence counts for samples analysed in the paper and the taxa identified using morphology These files are called in the r code (2) below.R Code: 1_CPR_Read_in_Fasta_filesR code for initial processing of the DNA sequence data and assignment of taxonomic OTUs1_CPR_Read_in_Fasta_files.rR Code: 2_Paper_AnalysisR code for looking at the data in more detail and used to produce the plots for the paper2_Paper_Analysis.r
DOI: 10.5061/dryad.8n8t0
title: Data from: Genomic divergence across ecological gradients in the Central African rainforest songbird (Andropadus virens)

description: The little greenbul, a common rainforest passerine from sub-Saharan
 Africa, has been the subject of long-term evolutionary studies to
 understand the mechanisms leading to rainforest speciation. Previous
 research found morphological and behavioural divergence across
 rainforest–savannah transition zones (ecotones), and a pattern of
 divergence with gene flow suggesting divergent natural selection has
 contributed to adaptive divergence and ecotones could be important areas
 for rainforests speciation. Recent advances in genomics and environmental
 modelling make it possible to examine patterns of genetic divergence in a
 more comprehensive fashion. To assess the extent to which natural
 selection may drive patterns of differentiation, here we investigate
 patterns of genomic differentiation among populations across environmental
 gradients and regions. We find compelling evidence that individuals form
 discrete genetic clusters corresponding to distinctive environmental
 characteristics and habitat types. Pairwise FST between populations in
 different habitats is significantly higher than within habitats, and this
 differentiation is greater than what is expected from geographic distance
 alone. Moreover, we identified 140 SNPs that showed extreme
 differentiation among populations through a genomewide selection scan.
 These outliers were significantly enriched in exonic and coding regions,
 suggesting their functional importance. Environmental association analysis
 of SNP variation indicates that several environmental variables, including
 temperature and elevation, play important roles in driving the pattern of
 genomic diversification. Results lend important new genomic evidence for
 environmental gradients being important in population differentiation.
description: fasta consensus
 sequences of RAD loci35,152 fasta sequences
 of final RAD loci assembled from our dataset. Filters are described in the
 methods and summarized in supplemental Table S2.RADtag_consensus_sequence.fa.gzVCF file containing bi-allelic SNPsVCF file contains 255,290 bi-allelic SNPs identified from RADseq data from 182 samples using stacks pipeline. SNPs are not filtered by minor allele frequency.greenbul.vcf.gzSample informationpopulation and habitat information of samples.Sample_Info.txt
DOI: 10.5061/dryad.vg4d4
title: Data from: Regulation of transposable elements: interplay between TE-encoded regulatory sequences and host-specific trans-acting factors in Drosophila melanogaster

description: Transposable elements (TEs) are mobile genetic elements that can move
 around the genome, and their expression is one precondition for this
 mobility. Because the insertion of TEs in new genomic positions is largely
 deleterious, the molecular mechanisms for transcriptional suppression have
 been extensively studied. In contrast, very little is known about their
 primary transcriptional regulation. Here, we characterize the expression
 dynamics of TE families in Drosophila melanogaster across a broad
 temperature range (13–29°C). In 71% of the expressed TE families, the
 expression is modulated by temperature. We show that this
 temperature-dependent regulation is specific for TE families and strongly
 affected by the genetic background. We deduce that TEs carry
 family-specific regulatory sequences, which are targeted by host-specific
 trans-acting factors, such as transcription factors. Consistent with the
 widespread dominant inheritance of gene expression, we also find the
 prevailing dominance of TE family expression. We conclude that TE family
 expression across a range of temperatures is regulated by an interaction
 between TE family-specific regulatory elements and trans-acting factors of
 the host.
description: scripts_and_data_TE_paperThese are all the protcolos used and results produced for the paper "Regulation of transposable elements: interplay between TE-encoded regulatory sequences and host-specific trans-acting factors in Drosophila melanogaster" by Ana Marija Jaksic, Robert Kofler and Christian Schlötterer. I did not include some intermediate files (for example intermediate fasta files or pileups) due to space reasons but they can be generated with the provided code. In file "hello.txt" you will find a shortcut to most important data and scripts. AM :)TE_paper_for_dryad.zip
DOI: 10.5061/dryad.52mc5
title: Data from: Predictions of response to temperature are contingent on model choice and data quality

description: The equations used to account for the temperature dependence of biological
 processes, including growth and metabolic rates are the foundations of our
 predictions of how global biogeochemistry and biogeography change in
 response to global climate change. We review and test the use of 12
 equations used to model the temperature dependence of biological processes
 across the full range of their temperature response, including supra- and
 sub-optimal temperatures. We focus on fitting these equations to thermal
 response curves for phytoplankton growth, but also tested the equations on
 a variety of traits across a wide diversity of organisms. We found that
 many of the surveyed equations have comparable abilities to fit data and
 equally high requirements for data quality (number of test temperatures
 and range of response captured), but lead to different estimates of
 cardinal temperatures and of the biological rates at these temperatures.
 When these rate estimates are used for biogeographic predictions,
 differences between the estimates of even the best fitting models can
 exceed the global biological change predicted for a decade of global
 warming. As a result, studies of the biological response to global changes
 in temperature must make careful consideration of model selection and of
 the quality of the data used for parametrizing these models.
description: Temperature
 responseData and analysis
 scripts in R. Data from published sources not included.temperature_response
 dryad.zip
DOI: 10.5061/dryad.4ps2t
title: Data from: A newly recognised species that has been confused with the global polyphagous pest scale insect, Coccus hesperidum Linnaeus (Hemiptera: Coccomorpha: Coccidae)

description: Coccus hesperidum L. (Hemiptera: Coccomorpha: Coccidae), the type species
 of the soft scale genus Coccus L., the family Coccidae and the whole of
 the scale insects (Coccoidea), is a cosmopolitan plant pest. Using DNA
 sequence data and morphological comparisons, we determine that there is a
 distinct species that is morphologically very similar to C. hesperidum.
 Here, we describe the species as Coccus praetermissus Lin & Tanaka
 sp. n., based on adult female specimens from Australia, Malaysia and
 Thailand. The adult female of C. praetermissus sp. n. differs from C.
 hesperidum in having dorsal setae with bluntly rounded tips, whereas they
 are sharply pointed in C. hesperidum. A detailed description of the newly
 recognised species is provided, incorporating adult female morphology and
 DNA sequences from mitochondrial and nuclear loci. Our examination of
 slides from The Natural History Museum, London, and several Australian
 institutions indicates that C. praetermissus sp. n. has been confused
 sometimes with C. hesperidum s. s. These findings have potential relevance
 to plant biosecurity and quarantine because C. hesperidum is cosmopolitan
 whereas C. praetermissus sp. n., which is also polyphagous and the two
 species can share many host plants, currently appears to be more
 geographically restricted. Additionally, there is deep genetic divergence
 within C. praetermissus sp. n. that might indicate that it is a cryptic
 species complex, but wider geographic sampling is required to test this
 possibility.
description: Lin_etal_2017_praetermissus_Appendix1Lin_etal_2017_praetermissus_Appendix2Lin_etal_2017_praetermissus_Appendix3Lin_etal_2017_praetermissus_FigS1Lin_etal_2017_praetermissus_FigS2Lin_etal_2017_praetermissus_FigS3Lin_etal_2017_praetermissus_FigS4
DOI: 10.5061/dryad.7v928
title: Data from: Development of the neurons controlling fertility in humans: new insights from 3D imaging and transparent fetal brains

description: Fertility in mammals is controlled by hypothalamic neurons that secrete
 gonadotropin-releasing hormone (GnRH). These neurons differentiate in the
 olfactory placodes during embryogenesis and migrate from the nose to the
 hypothalamus before birth. Information regarding this process in humans is
 sparse. Here, we adapted new tissue-clearing and whole-mount
 immunohistochemical techniques to entire human embryos/fetuses to
 meticulously study this system during the first trimester of gestation in
 the largest series of human fetuses examined to date. Combining these
 cutting-edge techniques with conventional immunohistochemistry, we provide
 the first chronological and quantitative analysis of GnRH neuron origins,
 differentiation and migration, as well as a 3D atlas of their distribution
 in the fetal brain. We reveal not only that the number of
 GnRH-immunoreactive neurons in humans is significantly higher than
 previously thought, but that GnRH cells migrate into several
 extrahypothalamic brain regions in addition to the hypothalamus. Their
 presence in these areas raises the possibility that GnRH has
 non-reproductive roles, creating new avenues for research on GnRH
 functions in cognitive, behavioral and physiological processes.
description: Movie S1 related to
 Figure 33D movie of high
 magnification of an optically cleared head of a CS 19 embryo labeled with
 anti-GnRH and anti-Peripherin antibodies.Movie
 S1.mp4Movie S2 related to
 Figure 43D movie of an optically
 cleared CS 21 head labeled for GnRH.Movie
 S2.mp4Movie S3 related to
 Figure 4C, D3D movie of an optically
 cleared GW 9.5 nose labeled for GnRH and TAG-1.Movie
 S3.mp4Movie S4 related to
 Figure 6AMovie of a
 3D-reconstruction of a GW 9 brain.Movie
 S4.mp4Movie S5 related to
 Figure S2Movie of a
 3D-reconstruction of a GW 12 brain.Movie
 S5.mp4Movie S6 related to
 Figure 6B-GMovie of an optically
 cleared E16.5 mouse embryo immunostained for GnRH.Movie
 S6.mp4Movie S7 related to
 Figure 7A-CMovie of an optically
 cleared P90 male mouse brain hemisphere immunostained for
 GnRH.Movie
 S7.mp4Movie S8 related to
 Figure 7DMovie of an optically
 cleared P90 male mouse olfactory bulb immunostained for
 GnRH.Movie
 S8.mp4
DOI: 10.5061/dryad.2j9p4
title: Data from: Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network

description: Patterning of body parts in multicellular organisms relies on the
 interpretation of transcription factor (TF) concentrations by genetic
 networks. To determine the extent by which absolute TF concentration
 dictates gene expression and morphogenesis programs that ultimately lead
 to patterns in Drosophila embryos, we manipulate maternally supplied
 patterning determinants and measure readout concentration at the position
 of various developmental markers. When we increase the overall amount of
 the maternal TF Bicoid 5-fold, Bicoid concentrations in cells at positions
 of the cephalic furrow, an early morphological marker, differ by a factor
 of two. This finding apparently contradicts the traditional
 threshold-dependent readout model, which predicts that the Bicoid
 concentrations at these positions should be identical. In contrast, Bicoid
 concentration at target gene expression boundaries is nearly unchanged
 during early developmental times, but adjusts dynamically toward the same
 2-fold change as development progresses. Thus the Drosophila segmentation
 gene network responds faithfully to Bicoid concentration during early
 development, in agreement with the threshold model, but subsequently
 partially adapts in response to altered Bicoid dosage, driving
 segmentation patterns towards their wild-type positions. This dynamic
 response requires other maternal regulators such as Torso and Nanos,
 suggesting that integration of maternal input information is not achieved
 through molecular interactions at the time of readout, but through the
 subsequent collective interplay of the network.
description: Liu et al. -
 LiveImaging_data_structureLiveImaging_data_structure.mat contains a data structure named "FlyLines" with Bicoid-GFP intensity gradient and cephalic furrow (CF) position measurements of fly embryos from live two-photon imaging for 29 fly lines.Liu et al. - Immunofluorescence_data_structureImmunoFluorescence_data_structure.mat contains a data structure named "Sessions" that contains raw gap ( Hb, Kr, Gt and Kni) and pair rule (Eve) gene expression (protein) intensity profiles measured using immunofluorescence imaging for fly embryos during n.c. 14 for 6 fly lines from our Bicoid-GFP fly line library.Liu et al. - BcdGFP_embryos_raw_dataHigh-resolution images of 28 embryos acquired by live two-photon microscopy; dorsal view, coronal plane (linear pixel dimension 0.46 micrometer). Embryos express Bcd-GFP fusion protein in a bcdE1 null mutant background (flyline 2XA). For 23 embryos two time points are provided: 16+/-2 min after mitosis 13 (for Bicoid gradient measurement) and 67+/-2 min after mitosis 13 (for cephalic furrow position measurement). Two additional embryos are provided for early time point (09 and 12); three additional embryos are provided for late time point (15, 24 and 28). Embryo 05 is missing from dataset. This dataset reproduces gradients in Figure 1C of main text.
DOI: 10.5061/dryad.7nh50k7
title: Data from: An association between differential expression and genetic divergence in the Patagonian olive mouse (Abrothrix olivacea)

description: Recent molecular studies have found striking differences between
 desert-adapted species and model mammals regarding water conservation. In
 particular, aquaporin 4, a classical gene involved in water regulation of
 model species, is absent or not expressed in the kidneys of desert-adapted
 species. To further understand the molecular response to water
 availability we studied the Patagonian olive mouse Abrothrix olivacea, a
 species with an unusually broad ecological tolerance that exhibits a great
 urine concentration capability. The species is able to occupy both the
 arid Patagonian steppe and the Valdivian and Magellanic forests. We
 sampled 95 olive mouse specimens from four localities (two in the steppe,
 two in the forests) and analyzed both phenotypic variables and
 transcriptomic data to investigate the response of this species to the
 contrasting environmental conditions. The relative size of the kidney and
 the ratio of urine to plasma concentrations were, as expected, negatively
 correlated with annual rainfall. Expression analyses uncovered nearly
 3,000 genes that were differentially expressed between steppe and forest
 samples and indicated that this species resorts to the “classical” gene
 pathways for water regulation. Differential expression across biomes also
 involves genes involved in immune and detoxification functions. Overall,
 genes that were differentially expressed showed a slight tendency to be
 more divergent and to display an excess of intermediate allele
 frequencies, relative to the remaining loci. Our results indicate that
 both differential expression in pathways involved in water conservation
 and geographical allelic variation are important in the occupation of
 contrasting habitats by the Patagonian olive mouse.
description: Reference
 transcriptomeAssemblage of the 26 new
 libraries was done using Trinity with default settings (Haas et al.
 2013)⁠. A reference transcriptome was constructed using the transcriptome
 assembly of each of the 26 samples and 13 previously published
 transcriptomic samples and multireads assembly (an assembly constructed
 joining the reads of 13 libraries) of Giorello et al. (2014)⁠, using
 custom python scripts. For the construction of the reference
 transcriptome, we select the best hit between the contigs, among the 39
 assembled transcriptomes, and the OMA browser mouse proteins (september
 2014 database) (Altenhoff et al. 2011)⁠⁠. The alignment was carried out
 using BLASTX (e-value cut offs &lt; 1e-10).Referencia_transcriptoma
DOI: 10.5061/dryad.p3b3f
title: Data from: NetView P: a network visualization tool to unravel complex population structure using genome-wide SNPs

description: Network-based approaches are emerging as valuable tools for the analysis
 of complex genetic structure in both wild and captive populations. NetView
 P combines data quality control with the construction of population
 networks based on mutual k-nearest-neighbours thresholds applied to
 genome-wide SNPs. The program is cross-platform compatible, open-source
 and efficiently operates on data ranging from hundreds to hundreds of
 thousands of SNPs through multiprocessing in Python. We used the pipeline
 for the analysis of pedigree data from simulated (n = 750, SNPs = 1279)
 and captive Silver-lipped Pearl Oysters (n = 415, SNPs = 1107), wild
 populations of the European Hake from the Atlantic and Mediterranean (n =
 834, SNPs = 380) and Gray Wolves from North America (n = 239, SNPs =
 86,103). The population networks effectively visualize large- and
 fine-scale genetic structure within and between populations, including
 family-level structure and relationships. NetView P comprises a
 network-based addition to other population analysis tools and provides
 user-friendly access to a complex network analysis pipeline through
 implementation in Python.
description: Oyster
 DataArchive containing data
 for P. maxima analysis with NetView P, including wild (n = 83, SNPs =
 999), captive (n = 684, SNPs = 834) and simulated (n = 3000, SNPs = 1271)
 genotypes, as well as input files (PED/MAP), node attributes and networks
 for visualization in Cytoscape.oyster_data.zip