cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vt25dc9
title: Data from: Evaluating the contribution of dispersal to community structure in Neotropical passerine birds

description: For two centuries evolutionary biologists have sought to explain elevated
 biodiversity in the Neotropics. Although different process are known to be
 important, it is still not uncommon for researchers to emphasize a single
 mechanism. Recently, arguments have highlighted the importance of
 dispersal shaping community structure and evolution across the region. We
 examine this hypothesis by visualizing spatial variation in community
 structure for the majority of South American passerines (Aves) across the
 northern half of South America. By sampling over a contiguous area we show
 how community structure varies widely across Amazonia and surrounding
 regions. Our results support a combination of processes including: the
 inability of species to disperse across geographic barriers, Andean
 uplift, and variation in habitat type. Although dispersal is a factor, our
 results emphasize a lack of dispersal, driven primarily by features of the
 landscape, coupled with historical changes in climate to be important
 drivers of Neotropical diversity.
description: 0.1.degree.comm.matrixR scriptsR scripts for the construction and analysis of the community matrixcommunity_matrix.zip
DOI: 10.5061/dryad.m1m0p
title: Data from: Aligner optimization increases accuracy and decreases compute times in multi-species sequence data

description: As sequencing technologies have evolved, the tools to analyze these
 sequences have made similar advances. However, for multi-species samples,
 we observed important and adverse differences in alignment specificity and
 computation time for bwa- mem (Burrows–Wheeler aligner-maximum exact
 matches) relative to bwa-aln. Therefore, we sought to optimize bwa-mem for
 alignment of data from multi-species samples in order to reduce alignment
 time and increase the specificity of alignments. In the multi-species
 cases examined, there was one majority member (i.e. Plasmodium falciparum
 or Brugia malayi) and one minority member (i.e. human or the Wolbachia
 endosymbiont wBm) of the sequence data. Increasing bwa-mem seed length
 from the default value reduced the number of read pairs from the majority
 sequence member that incorrectly aligned to the reference genome of the
 minority sequence member. Combining both source genomes into a single
 reference genome increased the specificity of mapping, while also reducing
 the central processing unit (CPU) time. In Plasmodium, at a seed length of
 18 nt, 24.1 % of reads mapped to the human genome using 1.7±0.1 CPU hours,
 while 83.6 % of reads mapped to the Plasmodium genome using 0.2±0.0 CPU
 hours (total: 107.7 % reads mapping; in 1.9±0.1 CPU hours). In contrast,
 97.1 % of the reads mapped to a combined Plasmodium–human reference in
 only 0.7±0.0 CPU hours. Overall, the results suggest that combining all
 references into a single reference database and using a 23 nt seed length
 reduces the computational time, while maximizing specificity. Similar
 results were found for simulated sequence reads from a mock metagenomic
 data set. We found similar improvements to computation time in a publicly
 available human-only data set.
description: Simulated Metagenomics
 Readsdryad.tar.gz
DOI: 10.5061/dryad.d1k3b
title: Data from: Repeated eye reduction events reveal multiple pathways to degeneration in a family of marine snails

description: Eye reduction occurs in many troglobitic, fossorial, and deep-sea animals
 but there is no clear consensus on its evolutionary mechanism. Given the
 highly conserved and pleiotropic nature of many genes instrumental to eye
 development, degeneration might be expected to follow consistent
 evolutionary trajectories in closely related animals. We tested this in a
 comparative study of ocular anatomy in solariellid snails from deep and
 shallow marine habitats using morphological, histological, and tomographic
 techniques, contextualized phylogenetically. Of 67 species studied, 15
 lack retinal pigmentation and at least seven have eyes enveloped by
 surrounding epithelium. Independent instances of reduction follow numerous
 different morphological trajectories. We estimate eye loss has evolved at
 least seven times within Solariellidae, in at least three different ways:
 characters such as pigmentation loss, obstruction of eye aperture, and
 “lens” degeneration can occur in any order. In one instance, two
 morphologically distinct reduction pathways appear within a single genus,
 Bathymophila. Even amongst closely related animals living at similar
 depths and presumably with similar selective pressures, the processes
 leading to eye loss have more evolutionary plasticity than previously
 realized. Although there is selective pressure driving eye reduction, it
 is clearly not morphologically or developmentally constrained as has been
 suggested by previous studies.
description: Supplementary Data
 Sumner-Rooney et al.Supplementary data files
 include all phylogenetic analyses (COI and combined gene trees),
 anatomical data (tomographic models of eight species) and full catalogue
 of specimens used in all aspects of this research.
DOI: 10.5061/dryad.rd55f
title: Data from: Comparing the prediction of joint species distribution models with respect to characteristics of sampling data

description: Biotic interactions have been rarely included in traditional species
 distribution models, wherein Joint Species Distribution Models (JSDMs)
 emerge as a feasible approach to incorporate environmental factors and
 interspecific interactions simultaneously, making it a powerful tool for
 analyzing the structure and assembly processes of biotic communities.
 However, the predictability and statistical robustness of JSDMs are
 largely unknown because of the lack of research efforts for those newly
 developed models. This study systematically evaluated the performances of
 five JSDMs in predicting the occurrence and biomass of multiple species,
 with a particular focus on diverse characteristics of sampling data,
 including type of response variables, number of sampling sites, and the
 number of species included in models. In general, most models yielded
 satisfactory performances on fitting to observed data and on the
 estimation of environmental effects; however, they showed less well
 performances in evaluating species associations, and their predictability
 had large variations. The JSDMs showed inconsistent performances between
 the goodness-of-fit and predictability in cross-validation, and the Boral
 model was relatively robust than others. The predictability of JSDMs was
 less influenced by sample sizes and substantially improved by
 incorporating rare species. This study contributes to an appropriate model
 selection and application of JSDMs.
description: Observation data for
 modellingThe file is in a form of
 R data, including all data used to fit the JSDMs, that is ,the biomass of
 multispecies and environmental variables of water temperature, salinity
 and depth.bio_env2.RDataJSDM modelsThe file can be read in R, including the full structure of the fitted models, BaysComm, Boral, Mistnet, HMSC, and Gjam.Models2.Rdata
DOI: 10.5061/dryad.j14r5
title: Data from: Evidence for amino acid snorkeling from a high-resolution, in vivo analysis of Fis1 tail anchor insertion at the mitochondrial outer membrane

description: Proteins localized to mitochondria by a carboxyl-terminal tail anchor (TA)
 play roles in apoptosis, mitochondrial dynamics, and mitochondrial protein
 import. To reveal characteristics of TAs that may be important for
 mitochondrial targeting, we focused our attention upon the TA of the
 Saccharomyces cerevisiae Fis1 protein. Specifically, we generated a
 library of Fis1p TA variants fused to the Gal4 transcription factor, then,
 using next-generation sequencing, revealed which Fis1p TA mutations
 inhibited membrane insertion and allowed Gal4p activity in the nucleus.
 Prompted by our global analysis, we subsequently analyzed the ability of
 individual Fis1p TA mutants to localize to mitochondria. Our findings
 suggest that the membrane-associated domain of the Fis1p TA may be
 bipartite in nature, and we encountered evidence that the positively
 charged patch at the carboxyl-terminus of Fis1p is required for both
 membrane insertion and organelle specificity. Furthermore, lengthening or
 shortening of the Fis1p TA by up to three amino acids did not inhibit
 mitochondrial targeting, arguing against a model in which TA length
 directs insertion of TAs to distinct organelles. Most importantly,
 positively charged residues were more acceptable at several positions
 within the membrane-associated domain of the Fis1p TA than negatively
 charged residues. These findings, emerging from the first high-resolution
 analysis of an organelle targeting sequence by deep mutational scanning,
 provide strong, in vivo evidence that lysine and arginine can
 "snorkel," or become stably incorporated within a lipid bilayer
 by placing terminal charges of their side chains at the membrane
 interface.
description: Keskin_AmpliconSequencingFis1TAA pool of plasmids containing Fis1p TA mutations in a Gal4-sfGFP-Fis1 fusion protein and constructed using degenerate primers was cultured in strain MaV203 for four generations in SC-Trp medium, SC-Ura medium, or SMM-Trp-His medium containing 0 mM, 5 mM, 10 mM, or 20 mM 3-AT. Plasmids present under each culture condition were then recovered from 10 OD600 units of cells. Primers 882 (TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGGTAGAGGATAAGATCCAGAAGGAAAC) and 883 (GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCATAAGAAATTCGCTTATTTAGAAGTG) were used to amplify the genomic region encoding the Fis1p TA from each plasmid pool. Using the provided PCR products, next-generation, paired-end sequencing was performed by Microsynth (Balgach, Switzerland) on a MiSeq Nano (2x150v2). GZIP-compressed FASTQ files and a commercial sequencing report are found in the associated ZIP file.
DOI: 10.5061/dryad.np7t1p2
title: Data from: Natural re-colonization and admixture of wolves (Canis lupus) in the US Pacific Northwest: challenges for the protection and management of rare and endangered taxa

description: Admixture resulting from natural dispersal processes can potentially
 generate novel phenotypic variation that may facilitate persistence in
 changing environments or result in the loss of population-specific
 adaptations. Yet, under the US Endangered Species Act, policy is limited
 for management of individuals whose ancestry includes a protected taxon;
 therefore, they are generally not protected under the Act. This issue is
 exemplified by the recently re-established grey wolves of the Pacific
 Northwest states of Washington and Oregon, USA. This population was likely
 founded by two phenotypically and genetically distinct wolf ecotypes:
 Northern Rocky Mountain (NRM) forest and coastal rainforest. The latter is
 considered potentially threatened in southeast Alaska and thus the source
 of migrants may affect plans for their protection. Genetic analysis
 revealed that the Washington wolves share ancestry with both wolf
 ecotypes, whereas the Oregon population shares ancestry with NRM forest
 wolves only. Using ecological niche modelling, we found that the Pacific
 Northwest states contain environments suitable for each ecotype, with wolf
 packs established in both environmental types. Continued migration from
 coastal rainforest and NRM forest source populations may increase the
 genetic diversity of the Pacific Northwest population. However, this
 admixed population challenges traditional management regimes given that
 admixture occurs between an adaptively distinct ecotype and a more
 abundant reintroduced interior form. Our results emphasize the need for a
 more precise US policy to address the general problem of admixture in the
 management of endangered species, subspecies, and distinct population
 segments.
description: filtered_variantSites_n126_callRate95_minDP10_GQ20Filtered variant call file (vcf format)Neutral regionsNeutral regions (canfam3.1; bed file format)neutralregions_canfam3.1.bed
DOI: 10.5061/dryad.ps56t
title: Data from: Genome-wide variation within and between wild and domestic yak

description: The yak is one of the few animals that can thrive in the harsh environment
 of the Qinghai-Tibetan Plateau and adjacent alpine regions. Yak provide
 essential resources allowing Tibetans to live at high altitudes. However,
 genetic variation within and between wild and domestic yak remain unknown.
 Here, we present a genome-wide study of the genetic variation within and
 between wild and domestic yak. Using next-generation sequencing
 technology, we re-sequenced three wild and three domestic yak with a mean
 of 5-fold coverage using our published domestic yak genome as a reference.
 We identified a total of 8.38 million SNPs (7.14 million novel), 383,241
 InDels and 126,352 structural variants between the six yak. We observed
 higher linkage disequilibrium in domestic yak than in wild yak and a
 modest but distinct genetic divergence between these two groups. We
 further identified more than a thousand of Potential Selected Regions
 (PSRs) for the three domestic yak by scanning the whole genome. These
 genomic resources can be further used to study genetic diversity and
 select superior breeds of yak and other bovid species.
description: variation in domestic
 and wild yakVariation information of
 wild and domestic yak: tar zxvf variation.tar.gz. The information is
 stored in GFF format (https://genome.ucsc.edu/FAQ/FAQformat.html#format3).
 There are three files: snp.gff: Single-nucleotide polymorphism information
 of six yak. indel.gff: Insertion and deletion information of six yak.
 sv.gff: structural variants of six yak.variation.tar.gzCustom perl scripts used in this articleCustomPerlScripts.tar.gz
DOI: 10.5683/sp3/5p83q0
title: Replication data for: Predicting Staphylococcus aureus spa Types Using MALDI-TOF Mass Spectrometry and Machine Learning.

description: This dataverse contains the datasets and R scripts for an article in preparation for submission.
DOI: 10.5061/dryad.t2q12
title: Data from: Can social partnerships influence the microbiome? insights from ant farmers and their trophobiont mutualists.

description: Mutualistic interactions with microbes have played a crucial role in the
 evolution and ecology of animal hosts. However, it is unclear what factors
 are most important in influencing particular host-microbe associations.
 While closely related animal species may have more similar microbiota than
 distantly related ones due to phylogenetic contingencies, social
 partnerships with other organisms, such as those in which one animal farms
 another, may also influence an organism’s symbiotic microbiome. We studied
 a mutualistic network of Brachymyrmex and Lasius ants farming several
 honeydew-producing Prociphilus aphids and Rhizoecus mealybugs to test
 whether the mutualistic microbiomes of these interacting insects are
 primarily correlated with their phylogeny or with their shared social
 partnerships. Our results confirm a phylogenetic signal in the microbiomes
 of aphid and mealybug trophobionts, with each species harboring
 species-specific endosymbiont strains of Buchnera (aphids), Tremblaya and
 Sodalis (mealybugs), and Serratia (both mealybugs and aphids) despite
 being farmed by the same ants. This is likely explained by strict vertical
 transmission of trophobiont endosymbionts between generations. In
 contrast, the ants’ microbiome is potentially shaped by their social
 partnerships, with ants that farm the same trophobionts also sharing
 strains of sugar-processing Acetobacteraceae bacteria, known from other
 honeydew-feeding ants and which likely reside extracellularly in the ants’
 guts. These ant-microbe associations are arguably more ‘open’ and subject
 to horizontal transmission or social transmission within ant colonies.
 These findings suggest that the role of social partnerships in shaping a
 host’s symbiotic microbiome can be variable, and is likely dependent on
 how the microbes are transmitted across generations.
description: Ivens et al. 2018 Mol.
 EcolAll data and scripts
 underlying figures and analyses presented in the publication and its
 supplements.
DOI: 10.5061/dryad.81jh5
title: Data from: A bee or not a bee: an experimental test of acoustic mimicry by hoverflies

description: The degree of similarity between Batesian mimics and their models varies
 widely and occurs across a range of sensory modalities. We use 3
 complementary experimental paradigms to investigate acoustic mimicry in
 hoverflies (Diptera: Syrphidae), which mimic stinging Hymenoptera. First,
 we analyze sounds made by 13 hoverfly species and 9 Hymenoptera species
 with and without simulated predation (“alarm” and “flight” sounds,
 respectively). We demonstrate that the bumblebees Bombus terrestris,
 Bombus hortorum, and Bombus lucorum and the hoverfly Cheilosia illustrata
 exhibit alarm sounds that are significantly different to their respective
 flight sounds, and indistinguishable between species. We then demonstrate
 that the B. terrestris alarm sound reduces predation on artificial prey by
 wild birds, but that the hoverfly mimic alarm sound does not. Finally, we
 trained chicks to avoid distasteful food in the presence of different
 acoustic stimuli. Overall, the chicks showed no difference in response to
 bee and hoverfly stimuli, demonstrating no innate aversion to the Bombus
 alarm sound. We therefore conclude that 1) similarity of acoustic signals
 exists among Hymenoptera and hoverflies, 2) acoustic aposematic signals
 (but not the almost identical mimetic signals) are effective at reducing
 predation, and 3) wild birds exhibit learned rather than innate aversion
 to certain acoustic stimuli.
description: Raw data on acoustic
 mimicryFull data from acoustic
 recordings of insect sounds, body sizes of specimens used, field predation
 data under different sound stimuli, and latency to attack from chicks
 trained on different stimuli. See ReadMe for more
 details.MooreHassallDryadData.xlsxHigh speed video of Bombus sound productionThe video shows the animal immobilised as described in the methods for the acoustic recording. There are two distinct phases of sound production: (i) 0:01 – 0:26 the insect flies in a characteristic manner with high amplitude wing strokes that produce a waveform similar to that seen in Figure S2A; (ii) 0:32 – 1:03 the insect responds to the simulated predation by transitioning to the alarm sound with nearly static wings and bodily contractions. It is suggested that this involves the decoupling of wings from the flight muscles similar to the mechanism of wing whirring that is used as a thermoregulatory mechanism in this species.EVT10.AVI
DOI: 10.5061/dryad.92gg5v0
title: Data from: Silk properties and overwinter survival in gregarious butterfly larvae

description: All organisms are challenged by encounters with parasites, which strongly
 select for efficient escape strategies in the host. The threat is
 especially high for gregarious species entering immobile periods, such as
 diapause. Larvae of the Glanville fritillary butterfly, Melitaea cinxia,
 spend the winter in diapause in groups of conspecifics each sheltered in a
 silk-nest. Despite intensive monitoring of the population, we have little
 understanding of the ecological factors influencing larval survival over
 the winter in the field. We tested whether qualitative and quantitative
 properties of the silk-nest contribute to larval survival over diapause.
 We used comparative proteomics, metabarcoding analyses, microscopic
 imaging, and in-vitro experiments to compare protein composition of the
 silk, community composition of the silk-associated microbiota, and silk
 density from both wild-collected and laboratory-reared families, which
 survived or died in the field. Although most traits assessed varied across
 families, only silk density correlated with over-winter survival in the
 field. The silk nest spun by gregarious larvae before the winter acts as
 an efficient breathable physical shield that positively affects larval
 survival during diapause. Such benefit may explain how this costly trait
 is conserved across populations of this butterfly species, and potentially
 across other silk-spinning insect species.
description: PostDiapause-silkDensityThis dataset includes measurements of up to two silk samples per nest A and B either under x500 magnification or x1000magnification under an electron microscope after platinum coatingPre-diapause-SilkDensityThis dataset includes measurements of one silk sample per nest under x500 magnification and x1000magnification under an electron microscope after platinum coatingInhibitionArea-Silk-Oct2017This dataset includes measurement of inhibition halos or growth area of silk-associated microbes in control or pathogen-inoculated plates in the labBombyxProtein composition of the silk and silk gland samples based on comparison with the Bombyx peptide databaseMCINXProtein composition of the silk and silk gland samples by comparison with the Glanville fritillary protein databaseScanning Electron Microscopy Images of Pre-diapause silkThese files are scanning electron microscopy pictures of silk samples collected at pre-diapause larval stage, either under x500 or x1000 magnification, in .TIFF formatPreDiapause-EM-Silk-Images.zipscanning Electron Microscopy Images of Post-diapause silkThis file contains all the Scanning electron micrographs of the silk samples collected at post-diapause larval stage, under x500 or x1000 magnififcationPostDiapause-EM-Silk-Images.zip
DOI: 10.5061/dryad.85sh7
title: Data from: "Diagnostic SNPs for inferring population structure in American mink (Neovison vison) identified through RAD sequencing" in Genomic Resources Notes accepted 1 October 2014 to 30 November 2014

description: The article documents the public availability of RAD sequencing data and
 generated SNPs for the American mink (Neovison vison). 224,095 polymorphic
 loci were identified from 14 mink from which primers were designed for a
 subset of 380 SNPs. The panel was tested on 211 mink. Fisher’s
 F-statistics (Fis, FIT and FST) as well as observed (HO), expected (HE)
 and unbiased expected (uHE) heterozygosity was calculated for the SNPs and
 194 SNPs was validated as being useful for population genetic studies.
description: Scriptsscripts from FASTX-toolkit for clipping, trimming and quality filter, as well as scripts for the ref map.pl. pipeline of Stacks (ustacks and sstacks) are available at Dryad data repository (http://dx.doi.org/10.5061/dryad.85sh7)scriptsbatch_1.catalog.tagsbatch_1.catalog.snpsbatch_1.catalog.allelesgenotypes of test population