cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kc835
title: Data from: Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity

description: Cultivated potato (Solanum tuberosum L.) is a highly heterozygous
 autotetraploid that presents challenges in genome analyses and breeding.
 Wild potato species serve as a resource for the introgression of important
 agronomic traits into cultivated potato. One key species is Solanum
 chacoense and the diploid, inbred clone M6, which is self-compatible and
 has desirable tuber market quality and disease resistance traits.
 Sequencing and assembly of the genome of the M6 clone of S. chacoense
 generated an assembly of 825,767,562 bp in 8,260 scaffolds with an N50
 scaffold size of 713,602 bp. Pseudomolecule construction anchored 508 Mb
 of the genome assembly into 12 chromosomes. Genome annotation yielded
 49,124 high confidence gene models representing 37,740 genes. Comparative
 analyses of the M6 genome with six other Solanaceae species revealed a
 core set of 158,367 Solanaceae genes and 1,897 genes unique to three
 potato species. Analysis of single nucleotide polymorphisms across the M6
 genome revealed enhanced residual heterozygosity on chromosomes 4, 8 and 9
 relative to the other chromosomes. Access to the M6 genome provides a
 resource for identification of key genes for important agronomic traits
 and aids in genome-enabled development of inbred diploid potatoes with the
 potential to accelerate potato breeding.
description: Readme.txt523_3_assembly_ALLPATHS_v4.1.fastaGenome assembly of S. chacoense M6, containing 8,260 scaffold sequencesM6_v4.1_PM.faPseudomolecules of S. chacoense M6, containing 12 chromosomesM6_v4.1_masked_PM.faMasked pseudomolecules of S. chacoense M6, containing 12 chromosomesM6_v4.1_scaffold.agpAGP file describing the assembly of S. chacoense M6 scaffolds within the pseudomoleculesM6_v4.1_PM_plus_chrUn.faPseudomolecules of S. chacoense M6, containing 12 chromosomes and chrUn (unanchored scaffolds)short_summary_BUSCO_output.txtOutput file from running BUSCO on the genome assemblyfull_table_BUSCO_output.tsvOutput file from running BUSCO on the genome assemblym6.hc.gene_models.chr_corrected.gff3Generic feature format file (gff3) of high-confidence genes in S. chacoense M6 (Corrected version as of 06/2018)m6.hc.gene_models.all_chrs_corrected.gff3Generic feature format file (gff3) of high-confidence genes in S. chacoense M6, including ChrUnpasa_m6.hc.gene_models.cdna.faTranscript sequences (cDNA) of high-confidence genes in S. chacoense M6pasa_m6.hc.gene_models.cds.faCoding sequences (CDS) of high-confidence genes in S. chacoense M6pasa_m6.hc.gene_models.pep.faProtein sequences of high-confidence genes in S. chacoense M6m6_gene_models.func_anno.txtFunctional annotation of working gene model set in S. chacoense M6pasa_m6.hc.gene_models.repr.pep.faProtein sequences of representative models of high-confidence genes in S. chacoense M6M6_gene_expression_matrix.xlsxExpression abundance of representative gene models523_3_assembly_ALLPATHS_v4.1.fasta.repeatmasker.gffGFF file of the repeat-masked genome
DOI: 10.5061/dryad.vmcvdncpc
title: Mating preferences can drive expansion or contraction of major histocompatibility complex gene family

description: Major histocompatibility complex (MHC)-based mating rules can evolve as a
 way to avoid inbreeding or to increase offspring immune competence. While
 the role of mating preference in shaping the MHC diversity in vertebrates
 has been acknowledged, its impact on individual MHC diversity has not been
 considered. Here, we use computer simulations to investigate how simple
 mating rules favouring MHC-dissimilar partners affect the evolution of the
 number of MHC variants in individual genomes, accompanying selection for
 resistance to parasites. We showed that the effect of such preferences
 could sometimes be dramatic. If preferences are aimed at avoiding
 identical alleles, the equilibrium number of MHC alleles is much smaller
 than under random mating. However, if the mating rule minimizes the ratio
 of shared to different alleles in partners, MHC number is higher than
 under random mating. Additionally, our simulations revealed that a
 negative correlation between the numbers of MHC variants in mated
 individuals can arise from simple rules of MHC-disassortative mating. Our
 results reveal unexpected potential of MHC-based mating preferences to
 drive MHC gene family expansions or contractions and highlight the need to
 study the mechanistic basis of such preferences, which is currently poorly
 understood.
description: The dataset contains results of computer simulations in the form
 of a swarm of text files. These text files can be analysed with Python
 script available at https://github.com/pbentkowski/MHC_Evolution/tree/MhcEvo2000/PyScripts .
description: File README.md contains an explanation of what data are in which
 directory.
DOI: 10.5061/dryad.jsxksn05j
title: Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea

description: How the microbiome interacts with hosts across evolutionary time is poorly
 understood. To address this question, datasets comprised of many host
 species are required to conduct comparative analyses. Here, we have
 analyzed 142 intestinal microbiome samples from 92 birds
 belonging to 74 species from Equatorial Guinea, using the 16S rRNA gene.
 Using four definitions for microbial taxonomic units (97%OTU, 99%OTU,
 99%OTU with singletons removed, ASV), we conducted alpha and beta
 diversity analyses and used phylogenetic comparative methods to assess the
 evolution of the microbiome as a trait of bird species. We find that raw
 abundances and diversity varied between the datasets but relative patterns
 were largely consistent across datasets. Host taxonomy, diet and locality
 were significantly associated with microbiomes, at generally similar
 levels using three distance metrics. Phylogenetic comparative methods were
 used to assess the relationship between the microbiome as a trait of a
 host species and the underlying bird phylogeny. We find that a neutral
 Brownian motion model does not explain variation in microbiomes. Instead,
 a White Noise model that indicates the trait contains little to no
 phylogenetic signal, is most likely across many definitions of
 "microbiome trait". While there was some support for the
 Ornstein-Uhlenbeck model (that invokes selection), the level of support
 was similar to our White Noise simulation, further supporting the White
 Noise model as the best explanation for the evolution of the microbiome as
 a trait of avian hosts. Our study highlights the qualitatively minor
 impact that different analytical choices can have on results and that
 biological interpretations can be robust to method choice.
description: Table 1. Sample information for the 92 individuals in this study.
 Fig.2 refers to the samples placement on Fig.2 in the manuscript. SampleID
 is the unique name given the sample, which is a combination of the first
 three letters of the genus, the first three letters of the species and the
 last three digits of the LSUMNS Bnumber given upon deposition to the
 museum (the full Bnumber for each specimen is 90XXX). The number of sample
 replicates (Sample Reps) and PCR replicates (PCR Reps) indicates which
 individuals had more than one sample taken. Other data are bird order,
 family, genus, species, sampling locality (see Fig. 1), sampling province,
 diet and weight (g).
DOI: 10.5061/dryad.x0k6djhfd
title: Extreme variation in testes size in an insect is linked to recent mating activity

description: Ample sperm production is essential for successful male reproduction in
 many species. The amount of sperm a male can produce is typically
 constrained by the size of his testes, which can be energetically
 expensive to grow and maintain. Whilst the economics of ejaculate
 allocation has been the focus of much theoretical and empirical
 literature, relatively little attention has been paid to individual adult
 variation and plasticity at the source of sperm production, the testes
 themselves. We experimentally address this issue using the insect Narnia
 femorata Stål (Hemiptera: Coreidae). We established the metabolic cost of
 testicular tissue, then quantified variation in individual testes mass in
 response to multiple mate quality and quantity treatments. We uncovered
 extreme variation across individuals and considerable short-term effects
 of mating activity on testes dry mass. Importantly, the observed variation
 in testes mass was associated with notable fitness consequences; females
 paired with males with larger testes had greater hatching success.
 Overall, pairing with a female resulted in a 11% reduction in dry testes
 mass. Despite this apparent considerable mating investment, we found no
 evidence of strategic allocation to higher quality females or longer-term
 changes in testes mass. The dynamic nature of testes mass and its
 metabolic cost is vital to consider in the context of re-mating rates,
 polyandry benefits and general mating system dynamics both in this species
 and more broadly.
description: ReadMe files included in upload
DOI: 10.15468/dl.khfttx
title: Occurrence Download

description: A dataset containing 1709 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Caenocoris nerii"
 ]
}

 The dataset includes 1709 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002062-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25338/b8w03p
title: Low coverage whole genomes of Calypte anna across California, USA

description: Recently, it was suggested that North America has lost nearly 30% of its
 avifauna since the 1970s.  To mitigate such avian population
 declines, many birds in California are protected under the Migratory Bird
 Treaty Act and California Fish and Game Code. Avian presence, therefore,
 at Caltrans infrastructure projects, especially bridge construction,
 has caused costly delays.  To avoid this
 conflict and understand population-specific migration
 and nesting patterns, we used Anna’s hummingbird, Calypte anna, (a species
 whose ecology has led to conflicts with construction in California) as a
 case study to assess population-level genetic variation across
 California, USA.  We sequenced whole genomes at low coverage from
 40 individuals across 9 California counties and assessed population
 differentiation.  This project initiates a general framework for
 assessing population-specific impacts of Caltrans projects on avian
 populations with the future goal of providing specific tools to
 avoid impacts with hummingbirds nesting on or around bridges. 
description: <i>Sample collection</i>
 <em>Calypte anna</em> hummingbirds were trapped using
 previously published methods (Bandivadekar et al., 2018) by master
 hummingbird banders. <i>DNA
 extraction</i> Whole genomic DNA was extracted
 from 100-150ml of blood stored in lysis buffer using the DNeasy Blood
 & Tissue Kit (Qiagen).  The following modifications to the
 extraction protocol were used: samples were incubated overnight at 56°C,
 the sample was passed over the spin column twice prior to washing, an
 extra column drying step was taken (14000rpm for 3min), and DNA was eluted
 in 200ml AE buffer heated to 56°C.  Whole genomic DNA was quantified using
 a Qubit Fluorometer and the quality of DNA was assessed using a 2% agarose
 gel. <i>Library preparation and
 sequencing</i> We used a modified library
 preparation based on Illumina’s Nextera protocol (Baym et al., 2015;
 Overgaard Therkildsen and Palumbi, 2017).  To start, genomic DNA was
 standardized to 3ng/ml then underwent a tagmentation step using TDE1
 enzyme and buffer (Illumina).  Dual combination Nextera indexes (Illumina)
 were then added to tagged DNA fragments followed by a reconditioning step
 using the Kapa HiFi Kit (Kapa Biosystems).  Libraries were then double
 size selected using AMPure XP Beads (Beckman Coulter) and quantified using
 a Qubit Fluorometer (Thermo Fisher Scientific).  Sixteen libraries only
 went through a left side selection. All libraries were
 pooled equimolarly then visualized with a Bioanalyzer (Agilent).  The
 pooled libraries were further size selected to 320-600bp fragments using a
 Blue Pippin (Sage Science) at the University of California, Davis Genome
 Center.  The final library was sequenced on an Illumina HiSeq with PE150
 and the resulting sequences were demultiplexed by Novogene (Sacramento,
 CA, USA).
DOI: 10.5061/dryad.ht76hdrbb
title: Interrelated ecological impacts of climate change on an apex predator

description: Climate change has broad ecological implications for species that rely on
 sensitive habitats. For some top predators, loss of habitat is expected to
 lead to cascading behavioral, nutritional, and reproductive changes that
 ultimately accelerate population declines. In the case of the polar bear
 (Ursus maritimus), declining Arctic sea ice reduces access to prey and
 lengthens seasonal fasting periods. We used a novel combination of
 physical-capture, biopsy darting, and visual aerial observation data to
 project reproductive performance for polar bears by linking sea-ice loss
 to changes in habitat use, body condition (i.e., fatness), and cub
 production. Satellite telemetry data from 43 (1991-1997) and 38
 (2009-2015) adult female polar bears in the Baffin Bay subpopulation
 showed that bears now spend an additional 30 days on land (90 days total
 in the 2000s compared to the 1990s), a change closely correlated with
 changes in spring sea-ice breakup and fall sea-ice formation. Body
 condition declined for all sex, age, and reproductive classes and was
 positively correlated with sea-ice availability in the current and
 previous year. Furthermore, cub litter size was positively correlated with
 maternal condition and spring breakup date (i.e., later breakup leading to
 larger litters), and negatively correlated with the duration of the
 ice-free period (i.e., longer ice-free periods leading to smaller
 litters). Based on these relationships we projected reproductive
 performance three polar bear generations into the future (approximately 35
 years). Results indicate that two-cub litters, previously the norm, could
 largely disappear from Baffin Bay as sea-ice loss continues. Our findings
 demonstrate how concurrent analysis of multiple data types collected over
 long periods from polar bears can provide a mechanistic understanding of
 the ecological implications of climate change. This information is needed
 for long-term conservation planning, which includes quantitative harvest
 risk assessments that incorporate estimated or assumed trends in future
 environmental carrying capacity.
DOI: 10.5061/dryad.7h44j0zqm
title: Data from: Disturbance-mediated consumer assemblages determine fish community structure and moderate top-down influences through bottom-up constraints

description: Disturbance is a strong structuring force that can influence the strength
 of species interactions at all trophic levels, but controls on the
 contributions to community structure of top-down and bottom-up processes
 across such gradients remain poorly understood. Changes in the composition
 of predator and consumer assemblages, and their associated traits, across
 gradients of environmental harshness (e.g., flooding) are likely to be a
 particularly important influence on the strength of top-down control and
 may drive bottom-up constraints. We examined how consumers with particular
 traits, and the predators that consumed them, varied across a gradient of
 stream flooding disturbance and used experiments to assess the predation
 impact on those contrasting consumer communities (ultimately quantifying
 how flood disturbance altered the strength of top-down control). Consumer
 community composition and mobility were strongly related to flood
 disturbance; the biomass and drift of protected primary consumers (i.e.,
 those with morphological defences) decreased with increasing flood
 disturbance. Predatory fish species had different disturbance niches, and
 path analysis identified that both direct flood-disturbance effects and
 indirect bottom-up constraints of flood-disturbance on consumers
 influenced predatory fish composition and biomass. Fishes generally fed
 most effectively on consumer types associated with their particular niche,
 but all fishes were strongly size-selective when feeding on protected
 consumers. Although protected consumers did not grow large enough to
 escape predation, an in situ experiment showed protected consumers were at
 a reduced risk of predation as disturbance increased compared to
 unprotected consumers. Overall, top-down control declined with flood
 disturbance, but the effect depended on consumer traits. Predatory fishes
 were only capable of exerting top-down control on protected consumers in
 benign habitats but impacted unprotected consumers across a larger range
 of the disturbance gradient. Collectively our findings suggest that a
 shift towards a more disturbed state will probably result in reduced
 predator impacts and a weakening of top-down control. Moreover, predicted
 increases in the frequency and intensity of climatic events causing
 disturbance, such as flooding, are likely to result in a community shift
 that disproportionately impacts protected consumers and the predators that
 utilise them as prey through the subsequent bottom-up constraints.
description: Excel file contains the following tabs:
 - Disturb vs Invert (drift&benth) -
 Disturbance vs Fish - Mesocosm predation expt
 - In situ predation expt
DOI: 10.5061/dryad.1vhhmgqpd
title: Marine species formation along the rise of Central America: the anomuran crab Megalobrachium

description: The evolution of marine neotropical shallow water species is expected to
 have been greatly affected by physical events related to the emergence of
 the Central American Isthmus. The anomuran crab Megalobrachium, a strictly
 neotropical porcellanid genus, consists of four species in the West
 Atlantic (WA) and nine in the East Pacific (EP). Dispersal is limited to a
 relatively short planktonic phase, which lasts approximately two weeks. We
 obtained DNA sequences of three mitochondrial and two nuclear genes of all
 but one species of Megalobrachium to construct a time-calibrated phylogeny
 of the genus and its historical phylogeography, based on the
 reconstruction of ancestral areas. The topology of the phylogenetic trees
 of Megalobrachium produced by Bayesian Inference (BI) and Maximum
 Likelihood (ML) were virtually congruent.  The genus is
 monophyletic with respect to other porcellanids. Ancestral area
 reconstruction indicates that it arose in the eastern Pacific 18 million
 years ago and diversified into at least 13 species that are currently
 formally recognized and three additional species indicated by our
 data.  Most morphological variation appears to have followed
 phylogenetic differentiation, though some cryptic speciation has also
 occurred. Four geminate clades in this genus implicate the gradual
 emergence of the Central American Isthmus in this diversification, but
 events preceding the final separation of the oceans as well as
 within-ocean events after the cessation of water connections were also
 important.
DOI: 10.5061/dryad.jm63xsj6c
title: Data from: Chromosome-level genome assembly of Paralithodes platypus provides insights into evolution and adaptation of king crabs

description: The blue king crab, Paralithodes platypus, which belongs to the Lithodidae
 family, is a commercially and ecologically important species. However, a
 high-quality reference genome for the king crab has not yet been reported.
 Here, we assembled the first chromosome-level blue king crab genome, which
 contains 104 chromosomes and an N50 length of 51.15 Mb. Furthermore, we
 determined that the large genome size can be attributed to the insertion
 of long interspersed nuclear elements and long tandem repeats. Genome
 assembly assessment showed that 96.54% of the assembled transcripts could
 be aligned to the assembled genome. Phylogenetic analysis showed the blue
 king crab to have a close relationship with the Eubrachyura crabs, from
 which it diverged 272.5 million years ago. Population history analyses
 indicated that the effective population of the blue king crab declined
 sharply and then gradually increased from the Cretaceous and Neogene
 periods, respectively. Furthermore, gene families related to developmental
 pathways, steroid and thyroid hormone synthesis, and inflammatory
 regulation, were expanded in the genome, suggesting that these genes
 contributed substantially to the environmental adaptation and unique body
 plan evolution of the blue king crab. The high-quality reference genome
 reported here provides a solid molecular basis for further study of the
 blue king crab’s development and environmental adaptation.
description: The genome of Paralithodes platypus
DOI: 10.5061/dryad.wm37pvmhf
title: Enhancement of flaky graphite cleaning by ultrasonic treatment

description: In this study, the aim is to simplify the graphite cleaning processing. In
 order to achieve flotation for graphite effectively, ultrasonic treatment
 was utilized as a pre-treatment technique. Flotation tests were conducted
 using for different ultrasound power and ultrasonic treatment time. The
 influences of ultrasonic treatment on particle sizes, morphologies,
 wettability, content of surface elements and on the flotation effect of
 flaky graphite were investigated. The results of ultrasonic treatment for
 graphite flotation were compared to the results of conventional flotation.
 The results showed that ultrasonic treatment not only changed the size of
 flaky graphite but also eliminated impurities on the graphite surface.
 Additionally, ultrasonic treatment improved the hydrophobicity of
 graphite. The effects of ultrasound were observed that it can remove not
 only silicate impurities but also most other metal impurities. The yield,
 carbon content and recovery of flotation concentrate were 91.46%, 95.17%
 and 96.12% after ultrasonic treatment for 4 minutes with ultrasound power
 1600W, which were 5.83%, 2.86% and 8.84% higher than that of conventional
 flotation, respectively. The graphite after ultrasonic treatment was
 conducted only one times flotation, the carbon content in concentrates
 products had reached
 95%.This study indicates that intensifying
 graphite flotation by ultrasonic treatment can shorten the graphite
 cleaning process.