cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.569qk
title: Data from: Subspecies delineation amid phenotypic, geographic, and genetic discordance in a songbird

description: Understanding the processes that drive divergence within and among species
 is a long-standing goal in evolutionary biology. Traditional approaches to
 assessing differentiation rely on phenotypes to identify intra- and
 interspecific variation, but many species express subtle morphological
 gradients in which boundaries among forms are unclear. This intraspecific
 variation may be driven by differential adaptation to local conditions and
 may thereby reflect the evolutionary potential within a species. Here, we
 combine genetic and morphological data to evaluate intraspecific variation
 within the Nelson's (Ammodramus nelsoni) and saltmarsh (A.
 caudacutus) sparrow complex, a group with populations that span
 considerable geographic distributions and a habitat gradient. We evaluated
 genetic structure among and within five putative subspecies of A. nelsoni
 and A. caudacutus using a reduced-representation sequencing approach to
 generate a panel of 1,929 SNPs among 69 individuals. Although we detected
 morphological differences among some groups, individuals sorted along a
 continuous phenotypic gradient. In contrast, the genetic data identified
 three distinct clusters corresponding to populations that inhabit coastal
 salt marsh, interior freshwater marsh, and coastal brackish-water marsh
 habitats. These patterns support the current species-level recognition but
 do not match the subspecies-level taxonomy within each species– a finding
 which may have important conservation implications. We identified loci
 exhibiting patterns of elevated divergence among and within these species,
 indicating a role for local selective pressures in driving patterns of
 differentiation across the complex. We conclude that this evidence for
 adaptive variation among subspecies warrants the consideration of
 evolutionary potential and genetic novelty when identifying conservation
 units for this group.
description: FASTQ file one of
 fourFASTQ input for
 Nelson's and Saltmarsh SparrowsSNPfileplaceholder1.fastq.gzFASTQ file two of fourRAD data for Nelson's and Saltmarsh SparrowsSNPfileplaceholder2.fastq.gzFASTQ file three of fourRAD data for Nelson's and Saltmarsh sparrowsSNPfileplaceholder3.fastq.gzFASTQ file four of fourRAD data for Nelson's and Saltmarsh SparrowsSNPfileplaceholder4.fastq.gzStacks output with identified variants in VCF formatVariants identified by Stacksall_loci.vcfMorphometric DataWeight, wing chord, and bill measurements for five subspecies comparisonsMorphometrics.xlsx
DOI: 10.5061/dryad.p2t8170
title: Data from: The origin of the odorant receptor gene family in insects

description: The origin of the insect odorant receptor (OR) gene family has been
 hypothesized to have coincided with the evolution of terrestriality in
 insects. Missbach et al. (2014) suggested that ORs instead evolved with an
 ancestral OR co-receptor (Orco) after the origin of terrestriality and the
 OR/Orco system is an adaptation to winged flight in insects. We
 investigated genomes of the Collembola, Diplura, Archaeognatha, Zygentoma,
 Odonata, and Ephemeroptera, and find ORs present in all insect genomes but
 absent from lineages predating the evolution of insects. Orco is absent
 only in the ancestrally wingless insect lineage Archaeognatha. Our new
 genome sequence of the zygentoman firebrat Thermobia domestica reveals a
 full OR/Orco system. We conclude that ORs evolved before winged flight,
 perhaps as an adaptation to terrestriality, representing a key
 evolutionary novelty in the ancestor of all insects, and hence a molecular
 synapomorphy for the Class Insecta.
description: Thermobia domestica
 genome assembly v 1.0The Thermobia domestica
 genome assembly is based on a single individual from a laboratory colony.
 Briefly, we sequenced the DNA extracted from a single T. domestica
 individual for assembly with the DISCOVAR v1 pipeline (Weisenfeld et al.,
 2014). Quality assessment of the resulting assembly was based on standard
 N statistics, k-mer distribution analysis, and the BUSCO v2 pipeline
 (Simão et al., 2015) as previously described (Brand et al.,
 2017).Tdom_v1.0.tgzOR sequences of annotated speciesFASTA format proteins for the newly described ORs of Ladona fulva, E. danica, T. domestica, M. hrabei. Suffixes, which are not part of the gene/protein name but indicate features of the gene model, are C – C-terminus missing, F – assembly was repaired, I – internal regions missing, J – gene model spans scaffolds, P – pseudogene.OR_sequences.faOR alignment used for gene tree reconstruction (Figure 2., Figure S2)CLUSTALX v2 alignment of all newly described ORs together with the 3 T. domestica ORs described by Missbach et al. 2014 and several neopteran Orcos.OR_alignment.fa
DOI: 10.5061/dryad.117hh
title: Data from: Evolution of sex determination loci in Atlantic salmon

description: Teleost fish exhibit a remarkable diversity in the control of sex
 determination, offering the opportunity to identify novel differentiation
 mechanisms and their ecological consequences. Here, we perform GWAS using
 4715 fish and 46,501 SNP to map sex determination to three separate
 genomic locations in Atlantic salmon (Salmo salar). To characterize each,
 whole genome sequencing was performed to 30-fold depth of coverage using
 20 fish representing each of three identified sex lineages. SNP
 polymorphism reveals male fish carry a single copy of the male specific
 region, consistent with an XX/XY or male heterogametric sex system.
 Haplotype analysis revealed deep divergence between the putatively
 ancestral locus on chromosome 2, compared with loci on chromosomes 3 and
 6. Haplotypes in fish carrying either the chromosome 3 or 6 loci were
 nearly indistinguishable, indicating a founding event that occurred
 following the speciation event that defines defined Salmo salar from other
 salmonids. These findings highlight the evolutionarily fluid state of sex
 determination systems in salmonids, and resolve to the sequence level
 differences in animals with divergent sex lineages.
description: Variant calls from 19
 Atlantic salmonVariant calls from 19
 Atlantic salmon against Solmo salar reference (ICSASG_v2 ) and a BAC
 contig covering the sdY region (NCBI accession
 KP898412)tas_salmon_19_dip.vcf.gz
DOI: 10.5061/dryad.q9474
title: Data from: Functional and evolutionary consequences of cranial fenestration in birds

description: Ostrich-like birds (Palaeognathae) show very little taxonomic diversity
 while their sister taxon (Neognathae) contains roughly 10000 species. The
 main anatomical differences between the two taxa are in the crania.
 Palaeognaths lack an element in the bill called the lateral bar that is
 present in both ancestral theropods and modern neognaths, have thin zones
 in the bones of the bill, and robust bony elements on the ventral surface
 of their crania. Here we use a combination of modelling and developmental
 experiments to investigate the processes that might have led to these
 differences. Engineering-based finite element analyses indicate that
 removing the lateral bars from a neognath increases mechanical stress in
 the upper bill and the ventral elements of the skull, regions that are
 either more robust or more flexible in palaeognaths. Surgically removing
 the lateral bar from neognath hatchlings led to similar changes. These
 results indicate that the lateral bar is load-bearing and suggest that
 this function was transferred to other bony elements when it was lost in
 palaeognaths. It is possible that the loss of the load-bearing lateral bar
 might have constrained diversification of skull morphology in palaeognaths
 and thus limited taxonomic diversity within the group.
description: Gussekloo_etal_Fenestration_EvolutionFinite Element Models in ANSYS format and measurement data of the in vivo experiment. For further information, please see included README files.
DOI: 10.5061/dryad.7294nh2
title: Data from: The future of cold-adapted plants in changing climates: Micranthes (Saxifragaceae) as a case study

description: As a result of changing climates, research has shown species undergoing
 range contractions and/or northward and higher elevational movements.
 Here, we evaluate how the distribution of a group of cold-adapted plant
 species with similar evolutionary histories changes in response to warming
 climates. We selected 29 species of Micranthes (Saxifragaceae)
 representing the mountain and Arctic biomes of the northern hemisphere.
 For this analysis, 24,755 data points were input into ecological niche
 models to assess both present fundamental niches and predicted future
 ranges under climate change scenarios. Comparisons were made across the
 Northern Hemisphere between all cold-adapted Micranthes, including Arctic
 species, montane species, and species defined as narrow endemics. Under
 future climate change models, 72% of the species would occupy smaller
 geographical areas than at present. This loss of habitat is most
 pronounced in Arctic species in general, but is also prevalent in species
 restricted to higher elevations in mountains. Additionally, narrow
 endemics species restricted to high elevations were more susceptible to
 habitat loss than those species found at lower elevations. By using a
 large dataset and modeling habitat suitability at a global scale, our
 results empirically model the threats to cold-adapted species as a result
 of warming climates. Although Arctic and alpine biomes share many
 underlying climate similarities, such as cold and short growing seasons,
 our results confirm that species in these climates have varied responses
 to climate change and that key abiotic variables differ between these two
 habitats.
description: custom_shape_filesCustom shapefiles for each species in the study. These shapefiles were made using a 2-degree buffer around every occurrence point and used to mask climate and soil layers.Occurance data in csvsOccurrence data used to construct shapefiles and train and test the ecological niche models. Cleaned and duplicates removed.occurance_data.zipRaster file of all Saxifragace Occurrence pointsRaster file of all Saxifragace Occurrence points used for making sampling bias file for each species and using in MaxEnt.all_saxifragaceae_raster.tifA-M_ecological_niche_model_resultsAscii files of present and future suitable habitat as predicted by Ecological niche models (sampling bias accounted for) for Micranthes species A-M.N-Z_ecological_niche_model_resultsAscii files of present and future habitat as generated by Ecological Niche Models for Micranthes species N-Z.
DOI: 10.5061/dryad.m4862mk
title: Data from: Selected HLA-B allotypes are resistant to inhibition or deficiency of the transporter associated with antigen processing (TAP)

description: Major histocompatibility complex class I (MHC-I) molecules present
 antigenic peptides to CD8+ T cells, and are also important for natural
 killer (NK) cell immune surveillance against infections and cancers. MHC-I
 molecules are assembled via a complex assembly pathway in the endoplasmic
 reticulum (ER) of cells. Peptides present in the cytosol of cells are
 transported into the ER via the transporter associated with antigen
 processing (TAP). In the ER, peptides are assembled with MHC-I molecules
 via the peptide-loading complex (PLC). Components of the MHC-I assembly
 pathway are frequently targeted by viruses, in order to evade host
 immunity. Many viruses encode inhibitors of TAP, which is thought to be a
 central source of peptides for the assembly of MHC-I molecules. However,
 human MHC-I (HLA-I) genes are highly polymorphic, and it is conceivable
 that several variants can acquire peptides via TAP-independent pathways,
 thereby conferring resistance to pathogen-derived inhibitors of TAP. To
 broadly assess TAP-independent expression within the HLA-B locus,
 expression levels of 27 frequent HLA-B alleles were tested in cells with
 deficiencies in TAP. Approximately 15% of tested HLA-B allotypes are
 expressed at relatively high levels on the surface of TAP1 or
 TAP2-deficient cells and occur in partially peptide-receptive forms and
 Endoglycosidase H sensitive forms on the cell surface. Synergy between
 high peptide loading efficiency, broad specificity for peptides prevalent
 within unconventional sources and high intrinsic stability of the empty
 form allows for deviations from the conventional HLA-I assembly pathway
 for some HLA-B*35, HLA-B*57 and HLA-B*15 alleles. Allotypes that display
 higher expression in TAP-deficient cells are more resistant to viral TAP
 inhibitor-induced HLA-I down-modulation, and HLA-I down-modulation-induced
 NK cell activation. Thus, unconventional antigen presentation pathways are
 broadly prevalent among HLA-B allotypes, and provide mechanisms to counter
 pathogen evasion strategies that target the conventional TAP-dependent
 HLA-I assembly pathway.
description: Figure
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 5Figure
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DOI: 10.5061/dryad.83s93
title: Data from: The influence of sea ice, wind speed and marine mammals on Southern Ocean ambient sound

description: This paper describes the natural variability of ambient sound in the
 Southern Ocean, an acoustically pristine marine mammal habitat. Over a
 3-year period, two autonomous recorders were moored along the Greenwich
 meridian to collect underwater passive acoustic data. Ambient sound levels
 were strongly affected by the annual variation of the sea-ice cover, which
 decouples local wind speed and sound levels during austral winter. With
 increasing sea-ice concentration, area and thickness, sound levels
 decreased while the contribution of distant sources increased. Marine
 mammal sounds formed a substantial part of the overall acoustic
 environment, comprising calls produced by Antarctic blue whales
 (Balaenoptera musculus intermedia), fin whales (Balaenoptera physalus),
 Antarctic minke whales (Balaenoptera bonaerensis) and leopard seals
 (Hydrurga leptonyx). The combined sound energy of a group or population
 vocalizing during extended periods contributed species-specific peaks to
 the ambient sound spectra. The temporal and spatial variation in the
 contribution of marine mammals to ambient sound suggests annual patterns
 in migration and behaviour. The Antarctic blue and fin whale contributions
 were loudest in austral autumn, whereas the Antarctic minke whale
 contribution was loudest during austral winter and repeatedly showed a
 diel pattern that coincided with the diel vertical migration of
 zooplankton.
description: Ambient sound data from
 mooring AWI_230_6A NetCDF file containing
 the ambient sound spectra and metadata from mooring
 AWI_230_6AWI_230_6_ambient_sound_data.ncAmbient sound data from mooring AWI_232_9A NetCDF file containing the ambient sound spectra and metadata from mooring AWI_232_9AWI_232_9_ambient_sound_data.ncMatlab code used to analyse and visualize the ambient sound dataThis Matlab code calculates the results and plots the figures presented in the paper. Step-by-step instructions are provided as comments in the code, as well as links to external data sets. The code was developed and tested using Matlab 2015a.ambient_sound_and_marine_mammal_contribution_data_analysis.m
DOI: 10.5061/dryad.g7356
title: Data from: Decrease in diversity and changes in community composition of arbuscular mycorrhizal fungi in roots of apple trees with increasing orchard management intensity across a regional scale

description: Understanding which factors drive the diversity and community composition
 of arbuscular mycorrhizal fungi (AMF) is important due to the role of
 these soil microorganisms in ecosystem functioning and current
 environmental threats to AMF biodiversity. Additionally, in
 agro-ecosystems, this knowledge may help to evaluate their use in making
 agriculture more sustainable. Here, we used 454-pyrosequencing of small
 subunit rRNA gene amplicons to quantify AMF diversity and community
 composition in the roots of cultivated apple trees across 24 orchards in
 central Belgium. We aimed at identifying the factors (soil chemical
 variables, organic versus conventional farming, and geographical location)
 that affect AMF diversity and community composition. In total, 110 AMF
 OTUs were detected, of which the majority belonged to the Glomeraceae
 (73%) and the Claroideoglomeraceae (19%). We show that soil
 characteristics and farming system, rather than the geographical location
 of the orchards, shape AMF communities on apple trees. Particularly,
 plant-available P content of the soil was associated with lower AMF
 diversity. In orchards with a lower plant-available P content of the soil
 (P &lt; 100 mg/kg soil), we also found a significantly higher AMF
 diversity in organically managed orchards as compared to conventionally
 managed orchards. Finally, the degree of nestedness of the AMF communities
 was related to plant-available P and N content of the soil, pointing at a
 progressive loss of AMF taxa with increasing fertilization. Overall, we
 conclude that a combination of organic orchard management and moderate
 fertilization may preserve diverse AMF communities on apple trees, and
 that AMF in the roots of apple trees appear not to be dispersal limited at
 the scale of central Belgium.
description: 1.sffSee
 readme.txt2.sffSee
 readme.txt3.sffSee
 readme.txt4.sffSee
 readme.txt
DOI: 10.6084/m9.figshare.31156873
title: Transcriptomic Atlas of the Maternal Mouse Olfactory Bulb Across Pregnancy and Lactation

description: <b>Overview：</b>This repository contains the raw and processed RNA-sequencing data, along with R scripts, associated with the manuscript: A time-series transcriptomic dataset of the mouse olfactory bulb across pregnancy and lactation.<b>Backgroud: </b>Olfaction is the primary sensory modality governing maternal behavior in rodents. To meet the demands of maternal care, the brain undergoes extensive and temporally dynamic plasticity during the perinatal period, particularly within the olfactory bulb (OB). This study generated a high-resolution transcriptomic dataset of the mouse OB to map molecular reprogramming events during reproduction. <b>Sample Information: </b>The dataset comprises transcriptomic profiles of adult female mice at five strategic time points (n=4 biologically independent replicates per group):<b>Vir: </b>Virgin / Non-pregnant controls.<b>E10.5: </b>Gestation Day 10.5 (Mid-pregnancy).<b>P0: </b>Parturition (Day of birth).<b>P7:</b> Postpartum Day 7.<b>P21: </b>Weaning (End of lactation).<b>File Inventory & Descriptions</b><b>Raw_Counts_Matrix.xlsx: </b>The raw integer read counts generated from bulk RNA-seq. Rows: Ensembl Gene IDs. Columns: 20 Samples (Vir, E10, P0, P7, P21; 4 replicates each).<b>TPM_Matrix_with_Annotations.xlsx:</b> Normalized gene expression matrix (Transcripts Per Million) including functional annotations. Rows: Ensembl IDs. Columns: TPM values for all 20 samples, and annotation columns (Gene Symbol, Description, GO Terms, KEGG Pathways).<b>Processing_DESeq2_and_PCA.R:</b> Loads raw counts, performs differential expression analysis using DESeq2, and executes Principal Component Analysis (PCA) to visualize sample clustering across reproductive stages.<b>Visualization_Volcano_Heatmaps_GO.R:</b> Generates figures: Pearson correlation heatmaps, Multi-group volcano plots, GO enrichment bubble plots, Targeted heatmaps for specific gene sets.
DOI: 10.6084/m9.figshare.31156873.v1
title: Transcriptomic Atlas of the Maternal Mouse Olfactory Bulb Across Pregnancy and Lactation

description: <b>Overview：</b>This repository contains the raw and processed RNA-sequencing data, along with R scripts, associated with the manuscript: A time-series transcriptomic dataset of the mouse olfactory bulb across pregnancy and lactation.<b>Backgroud: </b>Olfaction is the primary sensory modality governing maternal behavior in rodents. To meet the demands of maternal care, the brain undergoes extensive and temporally dynamic plasticity during the perinatal period, particularly within the olfactory bulb (OB). This study generated a high-resolution transcriptomic dataset of the mouse OB to map molecular reprogramming events during reproduction. <b>Sample Information: </b>The dataset comprises transcriptomic profiles of adult female mice at five strategic time points (n=4 biologically independent replicates per group):<b>Vir: </b>Virgin / Non-pregnant controls.<b>E10.5: </b>Gestation Day 10.5 (Mid-pregnancy).<b>P0: </b>Parturition (Day of birth).<b>P7:</b> Postpartum Day 7.<b>P21: </b>Weaning (End of lactation).<b>File Inventory & Descriptions</b><b>Raw_Counts_Matrix.xlsx: </b>The raw integer read counts generated from bulk RNA-seq. Rows: Ensembl Gene IDs. Columns: 20 Samples (Vir, E10, P0, P7, P21; 4 replicates each).<b>TPM_Matrix_with_Annotations.xlsx:</b> Normalized gene expression matrix (Transcripts Per Million) including functional annotations. Rows: Ensembl IDs. Columns: TPM values for all 20 samples, and annotation columns (Gene Symbol, Description, GO Terms, KEGG Pathways).<b>Processing_DESeq2_and_PCA.R:</b> Loads raw counts, performs differential expression analysis using DESeq2, and executes Principal Component Analysis (PCA) to visualize sample clustering across reproductive stages.<b>Visualization_Volcano_Heatmaps_GO.R:</b> Generates figures: Pearson correlation heatmaps, Multi-group volcano plots, GO enrichment bubble plots, Targeted heatmaps for specific gene sets.
DOI: 10.5061/dryad.81fv1
title: Data from: Ancestral whole genome duplication in the marine chelicerate horseshoe crabs

description: Whole-genome duplication (WGD) results in new genomic resources that can
 be exploited by evolution for rewiring genetic regulatory networks in
 organisms. In metazoans, WGD occurred before the last common ancestor of
 vertebrates, and has been postulated as a major evolutionary force that
 contributed to their speciation and diversification of morphological
 structures. Here, we have sequenced genomes from three of the four extant
 species of horseshoe crabs—Carcinoscorpius rotundicauda, Limulus
 polyphemus and Tachypleus tridentatus. Phylogenetic and sequence analyses
 of their Hox and other homeobox genes, which encode crucial transcription
 factors and have been used as indicators of WGD in animals, strongly
 suggests that WGD happened before the last common ancestor of these marine
 chelicerates &gt;135 million years ago. Signatures of
 subfunctionalisation of paralogues of Hox genes are revealed in the
 appendages of two species of horseshoe crabs. Further, residual homeobox
 pseudogenes are observed in the three lineages. The existence of WGD in
 the horseshoe crabs, noted for relative morphological stasis over
 geological time, suggests that genomic diversity need not always be
 reflected phenotypically, in contrast to the suggested situation in
 vertebrates. This study provides evidence of ancient WGD in the ecdysozoan
 lineage, and reveals new opportunities for studying genomic and regulatory
 evolution after WGD in the Metazoa.
description: C_rotundicauda_chelicerate_transcriptomeC_rotundicauda chelicerate transcriptome assembled using Trinity as described in accompanying manuscript. .fasta.gz file, needs unpacking using gzip or similar before useT_tridentatus_chelicerate_transcriptomeT. tridentatus chelicerate transcriptome assembled using Trinity as described in accompanying manuscript. .fasta.gz file, needs unzipping using gzip or similar before use.L_polyphemus_genome_contigs.faL polyphemus genome contigs assembled as described in accompanying manuscript. NB .fasta.gz file, needs to be unpacked using gzip or similar before useT_tridentatus_genome_contigs.faT_tridentatus genome contigs assembled as described in accompanying manuscript. NB .fasta.gz file, needs to be unpacked using gzip or similar before useC_rotundicauda_genome_contigs.faC_rotundicauda genome contigs assembled as described in accompanying manuscript. NB fasta.gz file, requires unpacking using gzip or similar before use