cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qv9s4mwb5
title: Sex-specific impact of inbreeding on pathogen load in the striped dolphin

description: The impact of inbreeding on fitness has been widely studied and provides
 consequential inference about adaptive potential and the impact on
 survival for reduced and fragmented natural populations. Correlations
 between heterozygosity and fitness are common in the literature, but they
 rarely inform about the likely mechanisms. Here we investigate a pathology
 with clear impact on health in striped dolphin hosts (a nematode infection
 that compromises lung function). Dolphins varied with respect to their
 parasite burden of this highly pathogenic lung nematode (Skrjabinalius
 guevarai). Genetic diversity revealed by high resolution restriction
 associated DNA (43,018 RADseq SNPs) analyses showed a clear association
 between heterozygosity and pathogen load, but only for female dolphins,
 for which the more heterozygous individuals had lower Skrjabinalius
 guevarai burden. One locus identified by RADseq was a strong outlier in
 association with parasite load (heterozygous in all uninfected females,
 homozygous for 94% of infected females), found in an intron of the Citron
 Rho-Interacting Serine/Theonine Kinase (CIT) locus (associated with milk
 production in mammals). Allelic variation at the Class II MHC DQB locus
 was also assessed and found to be associated with both regional variation
 and with pathogen load. Both sex specificity and the identification of
 associating functional loci provide insight into the mechanisms by which
 more inbred individuals may be more susceptible to the infection of this
 parasite.
description: Stranded animals. Amplification of the exon 2
 of the DQB1 locus of the Major Histocompatibillity Complex (MHC) Class
 II. ddRADseq analysis
DOI: 10.5061/dryad.kprr4xh1s
title: Altered 3D chromatin structure permits inversional recombination at the IgH locus

description: Immunoglobulin heavy chain (IgH) genes are assembled by two sequential DNA
 rearrangement events that are initiated by recombinase activating gene
 products (RAG) 1 and 2.  Diversity gene segments (DH) rearrange
 first, followed by variable (VH) gene rearrangements.  Here we
 provide evidence that each rearrangement step is guided by different rules
 of engagement between rearranging gene segments.  DH gene
 segments, that recombine by deletion of intervening DNA, must be located
 within a RAG1/2 scanning domain for efficient recombination.  In
 the absence of intergenic control region 1, a regulatory sequence that
 delineates the RAG scanning domain on WT IgH alleles, VH and DH gene
 segments can recombine with each other by both deletion and inversion of
 intervening DNA.  We propose that VH gene segments find their
 targets by diffusion-controlled mechanisms.  These distinct
 mechanisms may underlie differential allelic choice associated with each
 step of IgH gene assembly.
description: DJ<sub>H</sub>/VD<sub>H</sub>
 recombination assays were carried out as previously described.  Genomic
 DNA was purified from sorted bone marrow pro-B cells
 (IgM<sup>-</sup>B220<sup>+</sup>CD43<sup>+</sup>) from WT or IGCR1<sup>-/-</sup> mice.  5-fold serial dilutions of genomic DNA (200ng, 40ng, 8ng) were used to perform PCR to analyze DJ<sub>H</sub> rearrangements.  Primers used in this assay are listed in Table S5.  Primers flanking the <i>ROSA26</i> gene were used as a loading control under the same conditions.  GeneRuler 100 bp Plus (Thermo Fisher Scientific, #SM0324) was used to confirm sizes of PCR products. RAG2-deficient pro-B cell lines, CBE<sup>-/-</sup>(1), CBE<sup>-/-</sup>(2), WT, CBE<sup>-/-</sup>(1)/C1<sup>-/-</sup>#1, CBE<sup>-/-</sup>(1)/C1<sup>-/- </sup>#2, and CBE<sup>-/-</sup>(1)/C1<sup>-/-</sup>C2<sup>-/-</sup>,<sup> </sup>were infected with RAG2-expressing lentivirus, and cultured in complete medium with puromycin (Thermo Fisher Scientific, #A1113803, 2μg/ml).  After 14 days selection with puromycin, cells were harvested.  Genomic DNA was collected with DNeasy Blood & Tissue Kit (Qiagen, #69506), and the DNA was used to analyze DJ<sub>H</sub>/VDJ<sub>H</sub> rearrangements with HotStarTaq DNA Polymerase (Qiagen, #203205) as described as above. Amplification products were analyzed by agarose gel electrophoresis. 
description: Raw images are corresponded to Figures 2, 3, 5, S2 and S5 in the
 manuscript.
DOI: 10.5061/dryad.7sqv9s4pp
title: Arctic river dissolved and biogenic silicon exports - current conditions and future changes with warming

description: Silicon (Si) exports from terrestrial to marine systems can dictate
 phytoplankton species composition in Arctic coastal waters. Diatoms are
 often the dominant autotroph in Arctic waters, making Si an important
 control on Arctic marine primary productivity. Yet, even as Arctic regions
 are among the fastest warming on Earth, we lack baseline knowledge on the
 magnitudes and controls of Arctic river Si exports. To address
 uncertainties in current and future Si behavior, we used a combination of
 field data and modeling to quantify daily yields of dissolved Si (DSi) and
 biogenic Si (BSi) from a 400 km space‐for‐time latitudinal gradient of
 seven basins across the boreal‐Arctic transition in Alaska (USA) over the
 course of two years (2015‐2016). Mean annual DSi concentrations (33‐149
 μM) and yields (13‐49 kmol km‐2 yr‐1) were significantly and
 positively correlated with mean basin active layer depth, indicating that
 permafrost thaw will likely increase DSi fluxes to Arctic coastal waters.
 Conversely, BSi concentrations (7‐16 μM) and yields (2.6‐4.5 kmol
 km‐2 yr‐1) were more uniform across the seven basins, indicating
 that warming may not substantially alter BSi loads to coastal systems in
 the near future. Our data also indicate that climatic warming will advance
 the timing of Si delivery to coastal waters in the spring, although the
 ratios of Si to nitrogen in Arctic river exports will likely remain
 steady. These results highlight the important role of basin hydrology,
 largely driven by permafrost extent, as a key driver of Si exchange at the
 land‐sea interface in the Arctic.
description: Data includes concentration (units in micromolar, also
 indicated in spreadsheet) and flow data (area-normalized water yields in
 cubic meters per hour per square kilometer). Any missing cells or
 'NA's means that no data available for that sample.
DOI: 10.5061/dryad.34tmpg4gg
title: The Influence Law of Eccentric Load on the Performance of Yielding Bolt

description: In order to adapt high stress and large deformation of roadways, the
 prestressed yielding bolt has been developed. However, borehole deviation
 makes the boreholes out of perpendicular to the roadway surface, and the
 prestressed yielding bolt will be under eccentric load. In order to reveal
 the influence laws of eccentric load on the performance of the prestressed
 yielding bolt, the numerical simulation was carried out in this paper.
 Then, the influence of eccentric load on displacement-load relations, use
 efficiency for the yielding pipe material, plastic strains of the bolt
 components, as well as the absorptive capacity of the yielding pipe, were
 analyzed. The results are as follows: (1). Eccentric loads affected use
 efficiency of the yielding pipe material, plastic strains of bolt
 components and the absorptive capacity to a certain degree at the stage of
 initial displacement, while these impacts could be neglected at the stage
 of the later displacement; (2) Eccentric load mainly affected the yielding
 pipe’s displacement-load relations. As the eccentric load increased, the
 yielding point and its corresponding displacement increased linearly while
 the yielding amount decreased linearly; (3) The eccentric load could be
 adjusted to control the yielding point and amount in order to meet the
 roadway support’s requirement for the yielding bolt.
DOI: 10.5061/dryad.pc866t1k4
title: The sustainable development of coal mines by new cutting roof technology

description: China consumes more than 3.6 billion tons of coal every
 year, accounting for over 60% of the energy consumption. Therefore,
 the sustainable development of coal mine is a problem needed to be solved by the Chinese government. During the coal resources recovery, the protective coal pillars between the adjacent working faces cause the serious loss for coal resources. In order to solve the problem, it was put forward that the new technology of roof cutting with chain arm to retain roadway in the paper. Firstly, the process of retaining roadway, roof-cutting parameters and the damage ranges of roadway surrounding rock induced by roof cutting with chain arm were analyzed. Then, it was given that the working resistance of the temporary support equipment in technology of roof cutting with chain arm to retain roadway. Next, the roof-cutting height, the type of temporary support equipment, working resistance of portal support and support parameters of the bolt and anchor cables were optimized by the numerical calculation. Finally, the industrial experiment of retaining roadway by roof cutting with chain arm was carried out in a working face. The surrounding rock damage was minimal with the use of chain arm-roof cutting technology, and the variation range of the uniaxial compressive strength was only 5%, resulting in the roof damage rate to 82 mm. From the studies, it was concluded that this technology could be of a great asset to the coal mining community.
DOI: 10.5061/dryad.w0vt4b8mx
title: Origin of complexity in hemoglobin evolution

description: Most proteins associate into multimeric complexes with specific
 architectures, which often have functional properties like cooperative
 ligand binding, allosteric regulation, or the capacity to perform
 mechanical work. We have no detailed knowledge of how any multimer and its
 functions arose during historical evolution. Here we use ancestral protein
 reconstruction and biophysical assays to dissect the evolutionary origins
 of vertebrate hemoglobin (Hb), a heterotetramer of paralogous α and β
 subunits, which mediates oxygen transport and exchange by binding
 cooperatively to oxygen. We show that modern Hb evolved from an ancient
 monomer, characterize the historical “missing-link” dimeric form through
 which the modern tetramer evolved, and establish that two historical
 substitutions at this dimer’s protein surface were sufficient to confer
 tetramerization. Acquisition of this quaternary association dramatically
 alters the oxygen-binding function and confers cooperativity. These
 observations reveal that evolution can produce new molecular complexes and
 confer new functional properties via simple genetic mechanisms that
 recruit existing biophysical features into higher-level architectures.
description: See README file for further details
DOI: 10.5061/dryad.7h44j0zr3
title: A total-evidence dated phylogeny of Echinoidea combining phylogenomic and paleontological data

description: Phylogenomic and paleontological data constitute complementary resources
 for unravelling the phylogenetic relationships and divergence times of
 lineages, yet few studies have attempted to fully integrate them. Several
 unique properties of echinoids (sea urchins) make them especially useful
 for such synthetizing approaches, including a remarkable fossil record
 that can be incorporated into explicit phylogenetic hypotheses. We revisit
 the phylogeny of crown group Echinoidea using a total-evidence dating
 approach that combines the largest phylogenomic dataset for the clade, a
 large-scale morphological matrix with a dense fossil sampling, and a novel
 compendium of tip and node age constraints. To this end, we develop a
 novel method for subsampling phylogenomic datasets that selects loci with
 high phylogenetic signal, low systematic biases and enhanced clock-like
 behavior. Our results demonstrate that combining different data sources
 increases topological accuracy and helps resolve conflicts between
 molecular and morphological data. Notably, we present a new hypothesis for
 the origin of sand dollars, and restructure the relationships between stem
 and crown echinoids in a way that implies a long stretch of unidscovered
 evolutionary history of the crown in the late Paleozoic. Our efforts help
 bridge the gap between phylogenomics and phylogenetic paleontology,
 providing a model example of the benefits of combining the two.
DOI: 10.5061/dryad.0rxwdbrwb
title: A comparison of neutral genetic differentiation and genetic diversity among migratory and resident populations of Golden-crowned-Kinglets (Regulus satrapa)

description: Many animals migrate seasonally between breeding and non-breeding
 territories and these annual movements can have a profound effect on
 population genetic structure. We genotyped 283 individuals from 11
 populations at seven variable microsatellite loci and compared patterns of
 neutral genetic differentiation and neutral genetic diversity among
 migratory and resident breeding populations of the Golden-crowned Kinglet
 (Regulus satrapa), a widespread North American songbird. We predicted that
 resident populations would exhibit greater genetic differentiation and
 lower genetic diversity than migratory populations because migratory
 behaviour is thought to enhance gene flow. The magnitude of genetic
 differentiation and genetic diversity among migratory and resident
 populations was comparable, and the greatest levels of differentiation
 were observed for pairwise comparisons between Ontario and all western
 populations. Distance-based redundancy models and redundancy models
 revealed that patterns of neutral genetic differentiation and neutral
 genetic diversity follow an isolation-by-distance model and are not
 correlated with migratory behaviour. Overall it appears that genetic
 patterns are more closely associated with Pleistocene glacial history as
 proposed in a previous study.
description: The current dataset is genotype data for seven microsatellites.
 Included in this data are location, population information, latitude, and
 longitude for each sample. Missing geneotype values are listed as zero for
 this dataset.
DOI: 10.5061/dryad.7sqv9s4pq
title: Data from: Efficient summary statistics for detecting lineage fusion from phylogeographic datasets

description: Aim: Lineage fusion (merging of two or more populations of a species
 resulting in a single panmictic group) is a special case of secondary
 contact. It has the potential to counteract diversification and
 speciation, or to facilitate it through creation of novel genotypes.
 Understanding the prevalence of lineage fusion in nature requires reliable
 detection of it, such that efficient summary statistics are needed. Here
 we report on simulations that characterized the initial intensity and
 subsequent decay of signatures of past fusion for 17 summary statistics
 applicable to DNA sequence haplotype data. Location: Global. Taxon:
 Diploid out-crossing species. Methods: We considered a range of scenarios
 that could reveal the impacts of different combinations of read length
 versus number of loci (arrangement of DNA sequence data), and whether or
 not pre-fusion populations experienced bottlenecks coinciding with their
 divergence (historical context of fusion). Post-fusion gene pools were
 sampled along 10 successive time points representing increasing lag times
 following merging of sister populations, and summary statistic values were
 recalculated at each. Results: Many summary statistics were able to detect
 signatures of complete merging of populations after a sampling lag time of
 1.5 Ne generations, but the most informative ones included two neutrality
 tests and four diversity metrics, with ZnS being particularly powerful.
 Correlation was relatively low among the two neutrality tests and two of
 the diversity metrics. There were clear benefits of many short (200-bp ×
 200) loci over a handful of long (4-kb × 10) loci. Also, only the latter
 genetic dataset type was showed impacts of bottlenecks during divergence
 upon the number of informative summary statistics. Main conclusions: This
 work contributes to identifying cases of lineage fusion, and advances
 phylogeography by enabling more nuanced reconstructions of how individual
 species, or multiple members of an ecological community, responded to past
 environmental change.
description: Simulated DNA sequence data, generated using the software DIY-ABC
 v2.1.0 (Cornuet et al. 2014, <i>Bioinformatics</i>,
 30:1187–1189).
description: See "read me" files
 (README_for_Garrick_etal_2020_Simulated_Data.txt, and
 README_for_Garrick_etal_2020_Supplementary_Tables.txt).
DOI: 10.5061/dryad.c59zw3r3x
title: Data from: The evolution of parasite host range in heterogeneous host populations

description: Theory on the evolution of niche width argues that resource heterogeneity
 selects for niche breadth.  For parasites, this theory predicts
 that parasite populations will evolve, or maintain, broader host ranges
 when selected in genetically diverse host populations relative to
 homogeneous host populations.  To test this prediction, we
 selected the bacterial parasite Serratia marcescens to kill Caenorhabditis
 elegans in populations that were genetically heterogeneous (50% mix of two
 experimental genotypes) or homogeneous (100% of either
 genotype).  After 20 rounds of selection, we compared the host
 range of selected parasites by measuring parasite fitness (i.e. virulence,
 the selected fitness trait) on the two focal host genotypes and on a novel
 host genotype.  As predicted, heterogeneous host populations
 selected for parasites with a broader host range: these parasite
 populations gained or maintained virulence on all host
 genotypes.  This result contrasted with selection in homogeneous
 populations of one host genotype.  Here, host range contracted,
 with parasite populations gaining virulence on the focal host genotype and
 losing virulence on the novel host genotype.  This pattern was
 not, however, repeated with selection in homogeneous populations of the
 second host genotype: these parasite populations did not gain virulence on
 the focal host genotype, nor did they lose virulence on the novel host
 genotype.  Our results indicate that host heterogeneity can
 maintain broader host ranges in parasite populations.  Individual
 host genotypes, however, vary in the degree to which they select for
 specialization in parasite populations.
description: Counts of live hosts from mortality assays. Data entered from raw
 data sheets and mortality rate calculated in excel. Data analysis scripts
 included
description: Data analysis scripts included - this R file includes metadata
 for the two excel datasets
DOI: 10.5061/dryad.k98sf7m3g
title: Prioritising source populations for supplementing genetic diversity of reintroduced southern brown bandicoots Isoodon obesulus obesulus

description: Reintroduction programs can benefit from optimisation of source
 populations to maximise genetic diversity. Here, we report an approach to
 guide genetic supplementation of founder individuals to maximise genetic
 diversity in a reintroduction program for a nationally threatened
 Australian ground-dwelling marsupial, the southern brown bandicoot
 (eastern subspecies), Isoodon obesulus obesulus. Following local
 extinction ~ 100 years earlier, founding individuals were reintroduced to
 Booderee National Park in south-eastern Australia over three years from
 the nearest viable wild population, approximately 250 km to the south. To
 assess and manage risks associated with low genetic diversity, we measured
 genetic diversity of the reintroduced population relative to the diversity
 across the subspecies' range. The genetic diversity of the initial
 founder population was comparable with other sampled populations; most
 likely because (although few founders were used) the source population had
 high genetic diversity relative to other locations. We simulated scenarios
 of supplementation of the founder population from alternative candidate
 sources. We identified populations in the Melbourne region of Victoria as
 those that would yield the greatest increase in genetic diversity in the
 Booderee population. The simulated increase in diversity resulting from
 supplementation was accurately predicted by the pairwise FST contrast with
 the recipient population but not diversity of the supplementation source
 itself. Genetic diversity is an important consideration in
 reintroductions; our study enables managers to make informed decisions to
 maximise the long-term persistence and genetic diversity of reintroduced
 populations.
description: Raw SNP data for Isoodon obesulus obesulus before filtering,
 samples were genotyped using the DArTSeq method. Tab 1
 contains raw SNP genotypes provided by Diversity Arrays using the DArTSeq
 method. Data has not been filtered; Tab 2 contains Metadata code names for
 the SNP genotypes.
DOI: 10.5061/dryad.tqjq2bvvc
title: African wild dog dispersal and implications for management

description: Successful conservation of species that roam and disperse over large areas
 requires detailed understanding of their movement patterns and
 connectivity between subpopulations. But empirical information on
 movement, space use, and connectivity is lacking for many species, and
 data acquisition is often hindered when study animals cross international
 borders. The African wild dog (Lycaon pictus) exemplifies such species
 that require vast undisturbed areas to support viable, self‐sustaining
 populations. To study wild dog dispersal and investigate potential
 barriers to movements and causes of mortality during dispersal, between
 2016 and 2019 we followed the fate of 16 dispersing coalitions (i.e.,
 same‐sex group of ≥1 dispersing African wild dogs) in northern Botswana
 through global positioning system (GPS)‐satellite telemetry. Dispersing
 wild dogs covered ≤54 km in 24 hours and traveled 150 km to Namibia and
 360km to Zimbabwe within 10 days. Wild dogs were little hindered in their
 movements by natural landscape features, whereas medium to densely
 human‐populated landscapes represented obstacles to dispersal.
 Human‐caused mortality was responsible for &gt;90% of the recorded
 deaths. Our results suggest that a holistic approach to the management and
 conservation of highly mobile species is necessary to develop effective
 research and evidence‐based conservation programs across transfrontier
 protected areas, including the need for coordinated research efforts
 through collaboration between national and international conservation
 authorities.
description: GPS_locations_Dryad: This file contains GPS
 locations of the dispersing African wild dogs. Animal ID and Timestamps
 are linked to each random_identifier and available upon request to the
 leading author. Villages_CattlePosts_Fields:
 This file contains villages, cattle posts and crop fields in the
 vicinity of dispersing dog relocation data. This is not an exhaustive
 representation of all  villages, cattle posts and crop fields across the
 entire study area.
DOI: 10.5061/dryad.2v6wwpzj0
title: Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

description: Sustainable food production in the context of climate change necessitates
 diversification of agriculture and a more efficient utilization of plant
 genetic resources. Fonio millet (Digitaria exilis) is an orphan African
 cereal crop with a great potential for dryland agriculture. Here, we
 established high-quality genomic resources to facilitate fonio improvement
 through molecular breeding. These include a chromosome-scale reference
 assembly and deep re-sequencing of 183 cultivated and wild Digitaria
 accessions, enabling insights into genetic diversity, population
 structure, and domestication. Fonio diversity is shaped by climatic,
 geographic, and ethnolinguistic factors. Two genes associated with seed
 size and shattering showed signatures of selection. Most known
 domestication genes from other cereal models however have not experienced
 strong selection in fonio, providing direct targets to rapidly improve
 this crop for agriculture in hot and dry environments.