cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j8r8q
title: Data from: Genome-wide association studies in dogs and humans identify ADAMTS20 as a risk variant for cleft lip and palate

description: Cleft lip with or without cleft palate (CL/P) is the most commonly
 occurring craniofacial birth defect. We provide insight into the genetic
 etiology of this birth defect by performing genome-wide association
 studies in two species: dogs and humans. In the dog, a genome-wide
 association study of 7 CL/P cases and 112 controls from the Nova Scotia
 Duck Tolling Retriever (NSDTR) breed identified a significantly associated
 region on canine chromosome 27 (unadjusted p=1.1 x 10-13; adjusted p= 2.2
 x 10-3). Further analysis in NSDTR families and additional full sibling
 cases identified a 1.44 Mb homozygous haplotype (chromosome 27: 9.29 –
 10.73 Mb) segregating with a more complex phenotype of cleft lip, cleft
 palate, and syndactyly (CLPS) in 13 cases. Whole-genome sequencing of 3
 CLPS cases and 4 controls at 15X coverage led to the discovery of a
 frameshift mutation within ADAMTS20 (c.1360_1361delAA (p.Lys453Ilefs*3)),
 which segregated concordant with the phenotype. In a parallel study in
 humans, a family-based association analysis (DFAM) of 125 CL/P cases, 420
 unaffected relatives, and 392 controls from a Guatemalan cohort,
 identified a suggestive association (rs10785430; p =2.67 x 10-6) with the
 same gene, ADAMTS20. Sequencing of cases from the Guatemalan cohort was
 unable to identify a causative mutation within the coding region of
 ADAMTS20, but four coding variants were found in additional cases of CL/P.
 In summary, this study provides genetic evidence for a role of ADAMTS20 in
 CL/P development in dogs and as a candidate gene for CL/P development in
 humans.
description: UCD2014_Chr27_Critical_Interval_CanFam3.1UCD_2014.tfamPLINK GWAS fileUCD_2014.tpedPLINK tped format GWAS file
DOI: 10.5061/dryad.fr43s
title: Data from: Genome-wide SNP analysis reveals a genetic basis for sea-age variation in a wild population of Atlantic salmon (Salmo salar)

description: Delaying sexual maturation can lead to larger body size and higher
 reproductive success, but carries an increased risk of death before
 reproducing. Classical life history theory predicts that trade-offs
 between reproductive success and survival should lead to the evolution of
 an optimal strategy in a given population. However, variation in mating
 strategies generally persists, and in general, there remains a poor
 understanding of genetic and physiological mechanisms underlying this
 variation. One extreme case of this is in the Atlantic salmon (Salmo
 salar), which can show variation in the age at which they return from
 their marine migration to spawn (i.e. their “sea age”). This results in
 large size differences between strategies, with direct implications for
 individual fitness. Here, we used an Illumina Infinium SNP-array to
 identify regions of the genome associated with variation in sea age in a
 large population of Atlantic salmon in Northern Europe, implementing
 individual-based genome-wide association studies (GWAS) and
 population-based FST outlier analyses. We identified several regions of
 the genome which vary in association with phenotype and/or selection
 between sea ages, with nearby genes having functions related to muscle
 development, metabolism, immune response and mate choice. In addition, we
 found that individuals of different sea ages belong to different, yet
 sympatric populations in this system, indicating that reproductive
 isolation may be driven by divergence between stable strategies. Overall,
 this study demonstrates how genome-wide methodologies can be integrated
 with samples collected from wild, structured populations to understand
 their ecology and evolution in a natural context.
description: Data from: Genome-wide
 SNP analysis reveals a genetic basis for sea-age variation in a wild
 population of Atlantic salmon (Salmo salar)TenoSeaAgeDryadData.zip
DOI: 10.5061/dryad.b73kt
title: Data from: Consequences of divergence and introgression for speciation in Andean cloud forest birds

description: Divergence with gene flow is well documented and reveals the influence of
 ecological adaptation on speciation. Yet it remains intuitive that gene
 exchange inhibits speciation in many scenarios, particularly among
 ecologically similar populations. The influence of gene flow on the
 divergence of populations facing similar selection pressures has received
 less empirical attention than scenarios where differentiation is coupled
 with local environmental adaptation. I used a paired study design to test
 the influence of genomic divergence and introgression on plumage
 differentiation between ecologically similar allopatric replacements of
 Andean cloud forest birds. Through analyses of short-read genome-wide
 sequences from over 160 individuals in 16 co-distributed lineages, I found
 that plumage divergence is associated with deep genetic divergence,
 implicating a prominent role of geographic isolation in speciation. By
 contrast, lineages that lack plumage divergence across the same geographic
 barrier are more recently isolated or exhibit a signature of secondary
 genetic introgression, indicating a negative relationship between gene
 flow and divergence in phenotypic traits important to speciation. My
 results suggest that the evolutionary outcomes of cycles of isolation and
 divergence in this important theatre of biotic diversification are
 sensitive to time spent in the absence of gene flow.
description: SNP datasets,
 alignments, and tree filesIncluded: 1) .loci files
 output from pyRAD for each genus, used for D-statistic tests; 2) .str
 files output from pyRAD for each lineage (mono = monotypic, super =
 superspecies), used for Structure tests; 3) .phy files output from pyRAD
 for each lineage, used for RAxML analyses; 4).trees RAxML output files for
 each lineage; 5) .vcf files output from pyRAD for each genus, used for Fst
 calculations; 6) “_SNPS.gz” input files for Treemix analyses for each
 lineage.upload.zip
DOI: 10.5061/dryad.8ff71
title: Data from: Evolution of long centromeres in fire ants

description: Background: Centromeres are essential for accurate chromosome segregation,
 yet sequence conservation is low even among closely related species.
 Centromere drive predicts rapid turnover because some centromeric
 sequences may compete better than others during female meiosis. In
 addition to sequence composition, longer centromeres may have a
 transmission advantage. Results: We report the first observations of
 extremely long centromeres, covering on average 34 % of the chromosomes,
 in the red imported fire ant Solenopsis invicta. By comparison,
 cytological examination of Solenopsis geminata revealed typical small
 centromeric constrictions. Bioinformatics and molecular analyses
 identified CenSol, the major centromeric satellite DNA repeat. We found
 that CenSol sequences are very similar between the two species but the
 CenSol copy number in S. invicta is much greater than that in S. geminata.
 In addition, centromere expansion in S. invicta is not correlated with the
 duplication of CenH3. Comparative analyses revealed that several closely
 related fire ant species also possess long centromeres. Conclusions: Our
 results are consistent with a model of simple runaway centromere expansion
 due to centromere drive. We suggest expanded centromeres may be more
 prevalent in hymenopteran insects, which use haplodiploid sex
 determination, than previously considered.
description: output_TRF_SinvThe output file after running Tandem Repeat Finder (parameters: Match = 1, Mismatch = 1, Indel = 2, Probability of match = 80, Probability of indel = 5, Min score = 200, Max period = 750). The input sequences are from the draft genome of Solenopsis invicta (version H).Si_gnH_w_mitovms_v3.fa.1.1.2.80.5.200.750.datoutput_TRF_SgemThe output file after running Tandem Repeat Finder (parameters: Match = 1, Mismatch = 1, Indel = 2, Probability of match = 80, Probability of indel = 5, Min score = 200, Max period = 750). The input sequences are from the draft genome of Solenopsis geminata (unpublished data).k127m3_20140618.contigs.fa.1.1.2.80.5.200.750.datAdditional_file_1_monomer_sinvTandem repeat monomers extracted from the Solenopsis invicta genome using Tandem Repeat Finder.l_monomer_fasta.txtAdditional_file_2_monomer_sgemTandem repeat monomers extracted from the Solenopsis geminata genome using Tandem Repeat Finder.l_monomer_fasta.txtAdditional_file_3_censol_sinv_uniq_109The unique set of 109bp CenSol repeat sequences in the S. invicta genomeAdditional_file_4_censol_sgem_uniq_109The unique set of 109bp CenSol repeat sequences in the S. geminata genomeAdditional file 5_cloned CenSol repeatsCenSol repeat sequences cloned from the genome of Solenopsis invicta and Solenopsis geminataAdditional file 5.txt
DOI: 10.5061/dryad.081q1
title: Data from: Phylogeography in continuous space: coupling species distribution models and circuit theory to assess the effect of contiguous migration at different climatic periods on genetic differentiation in Busseola fusca (Lepidoptera: Noctuidae)

description: Current population genetic models fail to cope with genetic
 differentiation for species with large, contiguous and heterogeneous
 distribution. We show that in such a case, genetic differentiation can be
 predicted at equilibrium by circuit theory, where conductance corresponds
 to abundance in species distribution models (SDM). Circuit-SDM approach
 was used for the phylogeographic study of the lepidopteran cereal
 stemborer Busseola fusca Füller (Noctuidae) across sub-Saharan Africa.
 Species abundance was surveyed across its distribution range. SDM models
 were optimized and selected by cross validation. Relationship between
 observed matrices of genetic differentiation between individuals, and
 matrices of resistance distance was assessed through Mantel tests and
 redundancy discriminant analyses (RDA). A total of 628 individuals from
 130 localities in 17 countries were genotyped at 7 microsatellite loci.
 Six population clusters were found based on a Bayesian analysis. The
 eastern margin of Dahomey Gap between East and West Africa was the main
 factor of genetic differentiation. The SDM projections at present, last
 interglacial and last glacial maximum periods were used for estimation of
 circuit resistance between locations of genotyped individuals. For all
 periods of time, when using either all individuals or only East-African
 individuals, partial Mantel r and RDA analyses conditioning on geographic
 distance were found significant. Under future projections (year 2080),
 partial r and RDA significance were different. From this study, it is
 concluded that analytical solutions provided by circuit theory are useful
 for the evolutionary management of populations and for phylogeographic
 analysis when coalescence times are not accessible by approximate Bayesian
 simulations.
description: R script and data for
 the analysis of circuit-SDM modelThe archive contains in
 the root: A file "README.TXT" to do the analysis. And several
 files either described in the README file or coresponding to data files: a
 file "insect.csv" coresponding to per stem abundance of B. fusca
 across subsaharan localities for the optimisation of the species
 distribution models. A file "Busseola_fusca.asc" corresponding
 to maxent projection at present. A file "a_values" corresponding
 to individual Fst/(1-Fst) values among the genetic samples. There are 4
 directories: "Fit" contains de present worldclim data to fit the
 models. "Climatic_layers" contains the past and future climatic
 reconstrucitons. "maxent" contains the maxent projections.
 "cicuitscape" contains the circuitscape executables for cicuit
 resistance distance calculation.R_scripts_and_Data.zipgenetic_dataMicrosatellite datasample_locationsGeographic coordinates of the genetic samples
DOI: 10.5061/dryad.f5d20
title: Data from: The benefit of a tough skin: bullet holes, weathering and the preservation of heritage

description: Projectile damage to building stone is a widespread phenomenon. Sites
 damaged 100 years ago during the First World War still see daily use,
 while in a more contemporary setting numerous reports show the damage to
 buildings in Babylon, Mosul and Palmyra. While research has been carried
 out on the long-term effects of conflict such as fire damage, little is
 known about the protracted damage sustained through the impact of bullets,
 shrapnel and other metal projectiles outside of the field of engineering
 focused on ceramics and metals. To investigate alterations to mineral
 structure caused by projectile damage, impacts were created in
 medium-grained, well-compacted, mesoporous sandstone samples using 0.22
 calibre lead bullets shot at a distance of 20 m. Half these samples were
 treated with a surface consolidant (Wacker OH 100), to mimic natural
 cementation of the rock surface. These samples were then tested for
 changes to surface hardness and moisture movement during temperature
 cycles of 15–65°C. Petrographic thin section analysis was carried out to
 investigate the micro-scale deformation associated with high-speed impact.
 The results surprisingly show that stress build-up behind pre-existing
 cementation of the surface, as found in heritage sites that have been
 exposed to moisture and temperature fluctuations for longer periods of
 time, can be alleviated with a bullet impact. However, fracture networks
 and alteration of the mineral matrices still form a weak point within the
 structure, even at a relatively low impact calibre. This initial study
 illustrates the need for geomorphologists, geologists, engineers and
 heritage specialists to work collectively to gain further insights into
 the long-term impact of higher calibre armed warfare on heritage
 deterioration.
description: piccolo
 dataRock Surface Hardness
 dataL1_x4_ppl_engSample 1, image 1L1b_x4_cpl_engSample 1, image 2L2_2_x40_cpl_engSample 2, image 1L2_x4_cpl_engSample 2, image 2L2_x40_cpl_engSample 2, image 3L2-2_x4_cpl_engSample 2, image 4L3_x4_cpl_engSample 3, image 1L3_x4_ppl_engSample 3, image 2L3_x10_cpl_engSample 3, image 3L3-2_x10_cpl_engSample 3, image 4L4_2_x4_cpl_engSample 4, image 1L4_4x10_cpl_engSample 4, image 2L4-2_x10_cpl_engSample 4, image 3L5_x4_cpl_engSample 5, image 1L5_x10_cpl_engSample 5, image 2L6_2_x10_cpl_engSample 6, image 1L6_2x40_cpl_engSample 6, image 2L6_x4_cpl_engSample 6, image 3L6-3_x4_cpl_engSample 6, image 4L6_2_x4_ppl_engSample 7, image 1L6_3_x10_cpl_engSample 7, image 2L6_4_x4_cpl_engSample 7, image 3L8_x4_ppl_engSample 8, image 1L8_2_x40_ppl_engSample 8, image 2S3leftwwwenERT file, sample 3 lefthandsideS3middlewwwenERT file, sample 3 middle sectionS3rightwwwenERT file sample 3 righthandsideS7leftwwwenERT file sample 7 lefthandsideS7middlewwwenERT file sample 7 middle sectionS7rightwwwenDEERT file sample 7 righthandsideS7rightwwwen.dat
DOI: 10.5061/dryad.s5kp0
title: Data from: Signatures of positive selection in African Butana and Kenana dairy zebu cattle

description: Butana and Kenana are two types of zebu cattle found in Sudan. They are
 unique amongst African indigenous zebu cattle because of their high milk
 production. Aiming to understand their genome structure, we genotyped 25
 individuals from each breed using the Illumina BovineHD Genotyping
 BeadChip. Genetic structure analysis shows that both breeds have an
 admixed genome composed of an even proportion of indicine (0.75 ± 0.03 in
 Butana, 0.76 ± 0.006 in Kenana) and taurine (0.23 ± 0.009 in Butana, 0.24
 ± 0.006 in Kenana) ancestries. We also observe a proportion of 0.02 to
 0.12 of European taurine ancestry in ten individuals of Butana that were
 sampled from cattle herds in Tamboul area suggesting local crossbreeding
 with exotic breeds. Signatures of selection analyses (iHS and Rsb) reveal
 87 and 61 candidate positive selection regions in Butana and Kenana,
 respectively. These regions span genes and quantitative trait loci (QTL)
 associated with biological pathways that are important for adaptation to
 marginal environments (e.g., immunity, reproduction and heat tolerance).
 Trypanotolerance QTL are intersecting candidate regions in Kenana cattle
 indicating selection pressure acting on them, which might be associated
 with an unexplored level of trypanotolerance in this cattle breed. Several
 dairy traits QTL are overlapping the identified candidate regions in these
 two zebu cattle breeds. Our findings underline the potential to improve
 dairy production in the semi-arid pastoral areas of Africa through
 breeding improvement strategy of indigenous local breeds.
description: HD_dataThe High density SNP genotypes ped and map files are included. A phenotype file stating the sex and the breed type of all the cattle samples involved in the study is also included.The README file includes the 957 SNPs showing conflict annotations between UMD3.1 and Btau4.2
DOI: 10.5061/dryad.hv02n
title: Data from: The decay of motor adaptation to novel movement dynamics reveals an asymmetry in the stability of motion state-dependent learning

description: Motor adaptation paradigms provide a quantitative method to study
 short-term modification of motor commands. Despite the growing
 understanding of the role motion states (e.g., velocity) play in this form
 of motor learning, there is little information on the relative stability
 of memories based on these movement characteristics, especially in
 comparison to the initial adaptation. Here, we trained subjects to make
 reaching movements perturbed by force patterns dependent upon either limb
 position or velocity. Following training, subjects were exposed to a
 series of error-clamp trials to measure the temporal characteristics of
 the feedforward motor output during the decay of learning. The
 compensatory force patterns were largely based on the perturbation
 kinematic (e.g., velocity), but also showed a small contribution from the
 other motion kinematic (e.g., position). However, the velocity
 contribution in response to the position-based perturbation decayed at a
 slower rate than the position contribution to velocity-based training,
 suggesting a difference in stability. Next, we modified a previous model
 of motor adaptation to reflect this difference and simulated the behavior
 for different learning goals. We were interested in the stability of
 learning when the perturbations were based on different combinations of
 limb position or velocity that subsequently resulted in biased amounts of
 motion-based learning. We trained additional subjects on these combined
 motion-state perturbations and confirmed the predictions of the model.
 Specifically, we show that (1) there is a significant separation between
 the observed gain-space trajectories for the learning and decay of
 adaptation and (2) for combined motion-state perturbations, the gain
 associated to changes in limb position decayed at a faster rate than the
 velocity-dependent gain, even when the position-dependent gain at the end
 of training was significantly greater. Collectively, these results suggest
 that the state-dependent adaptation associated with movement velocity is
 relatively more stable than that based on position.
description: Exp_Data
DOI: 10.5061/dryad.3pq3q
title: Data from: Comparative transcriptomics of Entelegyne spiders (Araneae, Entelegynae), with emphasis on molecular evolution of orphan genes

description: Next-generation sequencing technology is rapidly transforming the
 landscape of evolutionary biology, and has become a cost-effective and
 efficient means of collecting exome information for non-model organisms.
 Due to their taxonomic diversity, production of interesting venom and silk
 proteins, and the relative scarcity of existing genomic resources, spiders
 in particular are excellent targets for next-generation sequencing (NGS)
 methods. In this study, the transcriptomes of six entelegyne spider
 species from three genera (Cicurina travisae, C. vibora, Habronattus
 signatus, H. ustulatus, Nesticus bishopi, and N. cooperi) were sequenced
 and de novo assembled. Each assembly was assessed for quality and
 completeness and functionally annotated using gene ontology information.
 Approximately 100 transcripts with evidence of homology to venom proteins
 were discovered. After identifying more than 3,000 putatively orthologous
 genes across all six taxa, we used comparative analyses to identify 24
 instances of positively selected genes. In addition, between ~ 550 and
 1,100 unique orphan genes were found in each genus. These unique,
 uncharacterized genes exhibited elevated rates of amino acid substitution,
 potentially consistent with lineage-specific adaptive evolution. The data
 generated for this study represent a valuable resource for future
 phylogenetic and molecular evolutionary research, and our results provide
 new insight into the forces driving genome evolution in taxa that span the
 root of entelegyne spider phylogeny.
description: Archive file of six
 spider transcriptome assembliesThis archive file
 contains Trinity transcriptome assemblies for six field-collected
 entelegyne spider species - Cicurina travisae, Cicurina vibora,
 Habronattus signatus, Habronattus ustulatus, Nesticus bishopi, and
 Nesticus cooperi.spider_transcriptome_assemblies.zip