cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p2n2d
title: Data from: Using network approaches to enhance the analysis of cross-linguistic polysemies

description: Since long it has been noted that cross-linguistically recurring
 polysemies can serve as an indicator of conceptual relations, and quite a
 few approaches to model and analyze such data have been proposed in the
 recent past. Although – given the nature of the data – it seems natural to
 model and analyze it with the help of network techniques, there are only a
 few approaches which make explicit use of them. In this paper, we show how
 the strict application of weighted network models helps to get more out of
 cross-linguistic polysemies than would be possible using approaches that
 are only based on item-to-item comparison. For our study we use a large
 dataset consisting of 1252 semantic items translated into 195 different
 languages covering 44 different language families. By analyzing the
 community structure of the network reconstructed from the data, we find
 that a majority of the concepts (68%) can be separated into 104 large
 communities consisting of five and more nodes. These large communities
 almost exclusively constitute meaningful groupings of concepts into
 conceptual fields. They provide a valid starting point for deeper analyses
 of various topics in historical semantics, such as cognate detection,
 etymological analysis, and semantic reconstruction.
description: SupMatThe supplemental
 material accompanying the study contains the word lists of all 195
 languages, upon which the reconstruction of the weighted network was
 based, and all essential results in form of text files, including the
 network, a detailed list and description of all inferred communities, and
 additional statistics regarding the languages.
DOI: 10.5061/dryad.011n0
title: Data from: Phylogenetic relationships within the lizard clade Xantusiidae: using trees and divergence times to address evolutionary questions at multiple levels

description: Xantusiidae (night lizards) is a clade of small-bodied, cryptic lizards
 endemic to the New World. The clade is characterized by several features
 that would benefit from interpretation in a phylogenetic context,
 including: (1) monophyletic status of extant taxa Cricosaura, Lepidophyma,
 and Xantusia; (2) a species endemic to Cuba (Cricosaura typica) of
 disputed age; (3) origins of the parthenogenetic species of Lepidophyma;
 (4) pronounced micro-habitat differences accompanied by distinct
 morphologies in both Xantusia and Lepidophyma; and (5) placement of
 Xantusia riversiana, the only vertebrate species endemic to the California
 Channel Islands, which is highly divergent from its mainland relatives.
 This study incorporates extensive new character data from multiple gene
 regions to investigate the phylogeny of Xantusiidae using the most
 comprehensive taxonomic sampling available to date. Parsimony and
 partitioned Bayesian analyses of more than 7 kb of mitochondrial and
 nuclear sequence data from 11 loci all confirm that Xantusiidae is
 monophyletic, and comprises three well-supported clades: Cricosaura,
 Xantusia, and Lepidophyma. The Cuban endemic Cricosaura typica is well
 supported as the sister to all other xantusiids. Estimates of divergence
 time indicate that Cricosaura diverged from the (Lepidophyma + Xantusia)
 clade ∼81 million years ago (Ma), a time frame consistent with the
 separation of the Antilles from North America. Our results also confirm
 and extend an earlier study suggesting that parthenogenesis has arisen at
 least twice within Lepidophyma without hybridization, that rock-crevice
 ecomorphs evolved numerous times (&gt;9) within Xantusia and
 Lepidophyma, and that the large-bodied Channel Island endemic X.
 riversiana is a distinct, early lineage that may form the sister group to
 the small-bodied congeners of the mainland.
description: 12SAlignment of existing
 (GenBank) and newly generated sequences.16SAlignment of existing
 (GenBank) and newly generated sequences.aenolaseAlignment of existing (GenBank) and newly generated sequences.BDNFAlignment of existing (GenBank) and newly generated sequences.CMOSAlignment of existing (GenBank) and newly generated sequences.CYTBAlignment of existing (GenBank) and newly generated sequences.GAPDAlignment of existing (GenBank) and newly generated sequences.ND4Alignment of existing (GenBank) and newly generated sequences.NT3Alignment of existing (GenBank) and newly generated sequences.POMCAlignment of existing (GenBank) and newly generated sequences.RAG1Alignment of existing (GenBank) and newly generated sequences.
DOI: 10.5061/dryad.m3h18
title: Data from: Genes and QTLs controlling inflorescence and stem branch architecture in Leymus (Poaceae: Triticeae) wildrye

description: Grass inflorescence and stem branches show recognizable architectural
 differences among species. The inflorescence branches of Triticeae cereals
 and grasses, including wheat, barley, and 400–500 wild species, are
 usually contracted into a spike formation, with the number of flowering
 branches (spikelets) per node conserved within species and genera.
 Perennial Triticeae grasses of genus Leymus are unusual in that the number
 of spikelets per node varies, inflorescences may have panicle branches,
 and vegetative stems may form subterranean rhizomes. Leymus cinereus and
 L. triticoides show discrete differences in inflorescence length,
 branching architecture, node number, and density; number of spikelets per
 node and florets per spikelet; culm length and width; and perimeter of
 rhizomatous spreading. Quantitative trait loci controlling these traits
 were detected in 2 pseudo-backcross populations derived from the
 interspecific hybrids using a linkage map with 360 expressed gene sequence
 markers from Leymus tiller and rhizome branch meristems. Alignments of
 genes, mutations, and quantitative trait loci controlling similar traits
 in other grass species were identified using the Brachypodium genome
 reference sequence. Evidence suggests that loci controlling inflorescence
 and stem branch architecture in Leymus are conserved among the grasses,
 are governed by natural selection, and can serve as possible gene targets
 for improving seed, forage, and grain production.
description: TTC Integrated Consensus
 MapIntegrated consensus map
 of the Leymus TTC1 and TTC2 mapping populations in MapQTL
 format.TTC1 BC1 Markers
 1574MapQTL genotype file for
 TTC1 population.TTC2 BC1 Markers
 1739MapQTL genotype file for
 TTC2 population.TTC1_Traits9bMapQTL traits file for Leymus TTC1 population.TTC2_Traits9bMapQTL trait file for Leymus TTC2 populationTTC1_QTL_IciMappingIciMapping data for Leymus TTC1 population.TTC2_QTL_IciMappingIciMapping file for Leymus TTC2 population.
DOI: 10.5061/dryad.7kn7r
title: Data from: Genome-wide association study of meat quality traits in a White Duroc × Erhualian F2 intercross and Chinese Sutai pigs

description: Thousands of QTLs for meat quality traits have been identified by linkage
 mapping studies, but most of them lack precise position or replication
 between populations, which hinder their application in pig breeding
 programs. To localize QTLs for meat quality traits to precise genomic
 regions, we performed a genome-wide association (GWA) study using the
 Illumina PorcineSNP60K Beadchip in two swine populations: 434 Sutai pigs
 and 933 F2 pigs from a White Duroc×Erhualian intercross. Meat quality
 traits, including pH, color, drip loss, moisture content, protein content
 and intramuscular fat content (IMF), marbling and firmness scores in the
 M. longissimus (LM) and M. semimembranosus (SM) muscles, were recorded on
 the two populations. In total, 127 chromosome-wide significant SNPs for
 these traits were identified. Among them, 11 SNPs reached genome-wise
 significance level, including 1 on SSC3 for pH, 1 on SSC3 and 3 on SSC15
 for drip loss, 3 (unmapped) for color a*, and 2 for IMF each on SSC9 and
 SSCX. Except for 11 unmapped SNPs, 116 significant SNPs fell into 28
 genomic regions of approximately 10 Mb or less. Most of these regions
 corresponded to previously reported QTL regions and spanned smaller
 intervals than before. The loci on SSC3 and SSC7 appeared to have
 pleiotropic effects on several related traits. Besides them, a few QTL
 signals were replicated between the two populations. Further, we
 identified thirteen new candidate genes for IMF, marbling and firmness, on
 the basis of their positions, functional annotations and reported
 expression patterns. The findings will contribute to further
 identification of the causal mutation underlying these QTLs and future
 marker-assisted selection in pigs.
description: Porcine 60K SNP
 genotypes for F2 and Sutai pigsDataset corresponds to
 the article: "Genome-wide Association Study of Meat Quality Traits in
 a White Duroc × Erhualian F2 intercross and Chinese Sutai Pigs" Junwu
 Ma, Lusheng Huang. For any correspondnce, please address Lusheng Huang
 (lushenghuang@hotmail.com). The tarred file "Porcine 60K SNP genotype
 of F2 and Sutai pigs.zip" contains 3 PLINK format files (.map and
 .ped). The first file "SNP60K_positions.map" gives the positions
 of 62163 SNPs (from the Illumina's Porcine SNP60 Beadchips) according
 to the Sscrofa10.2 assembly.The second file "F2_genotypes.ped"
 contains these SNPs genotypes for 939 F2 individuals derived from the
 White Duroc×Erhualian (WE) resource population. The third file
 "Sutai_genotypes.ped" contains these SNPs genotypes for 434
 Sutai pigs.Porcine 60K SNP genotype of F2
 and Sutai pigs.zip
DOI: 10.5061/dryad.4qk42
title: Data from: Upload any object and evolve it: injecting complex geometric patterns into CPPNs for further evolution

description: Ongoing, rapid advances in three-dimensional (3D) printing technology are
 making it inexpensive for lay people to manufacture 3D objects. However,
 the lack of tools to help non-technical users design interesting, complex
 objects represents a significant barrier preventing the public from
 benefitting from 3D printers. Previous work has shown that an evolutionary
 algorithm with a generative encoding based on developmental biology-a
 compositional pattern-producing network (CPPN)-can automate the design of
 interesting 3D shapes, but users collectively had to start each act of
 creation from a random object, making it difficult to evolve preconceived
 target shapes. In this paper, we describe how to modify that algorithm to
 allow the further evolution of any uploaded shape. The technical insight
 is to inject the distance to the surface of the object as an input to the
 CPPN. We show that this seeded-CPPN technique reproduces the original
 shape to an arbitrary resolution, yet enables morphing the shape in
 interesting, complex ways. This technology also raises the possibility of
 two new, important types of science: (1) It could work equally well for
 CPPN-encoded neural networks, meaning neural wiring diagrams from nature,
 such as the mouse or human connectome, could be injected into a neural
 network and further evolved via the CPPN encoding. (2) The technique could
 be generalized to recreate any CPPN phenotype, but substituting a flat
 CPPN representation for the rich, originally evolved one. Any evolvability
 extant in the original CPPN genome can be assessed by comparing the two, a
 project we take first steps toward in this paper. Overall, this paper
 introduces a method that will enable non-technical users to modify
 complex, existing 3D shapes and opens new types of scientific inquiry that
 can catalyze research on bio-inspired artificial intelligence and the
 evolvability benefits of generative encodings.
description: A Comparison of
 Generational Evolutionary Variation Between a Rich CPPN Genome and a Flat
 Seeded CPPN GenomeA comparison of
 evolutionary variation produced when evolving the “Angel with Halo” object
 from EndlessForms with two different CPPN representations: its original
 rich CPPN genome and a flat CPPN genome produced by the seeded-CPPN
 technique. Each picture represents a generation. The generations of
 objects produced by the original rich CPPN genome are in the
 'production' folder while the objects produced from the seeded
 CPPN are in the 'seed' folder. Each file is named under the
 following format 'genx_y_z_w.png', which represents the object
 (seeded or original, depending on folder) at generation x. To reach
 generation x+1 (for x &lt; 15) objects from positions y, z and w were
 chosen randomly to be the parents. Object position is indexed at 0 and
 increases from left to right and top to bottom (first row is 0-4,
 inclusive).dryad.zip
DOI: 10.5061/dryad.v04g2
title: Data from: Effects of two grass species on the composition of soil fungal communities

description: Many studies have shown effects of plants species on fungal communities,
 but these are often confounded with soil effects. Thus, the specific role
 of plant species in structuring rhizospheric and soil fungal communities
 is poorly described. Our study used microcosms in which plants were grown
 under artificial conditions to bridge this gap. Two perennial grasses
 dominating subalpine grasslands, Festuca paniculata and Dactylis
 glomerata, were grown at two levels of fertilization on standard soil.
 Fungal communities were determined by 454 pyrosequencing of the internal
 transcribed spacer 1 region. Among the fungal communities characterized by
 the primers used, original communities were associated to each plant
 species and also diverged between rhizosphere and bulk soils within each
 plant species, though there were no significant fertilization effects.
 Differences regarded global composition of the fungal communities and
 abundant molecular operational taxonomic units (MOTUs). Both plant species
 and location effects were reflected more in the abundance than in the
 composition of MOTUs. The observed differences in fungal communities
 coincide with differing strategies of plant root growth, with D. glomerata
 having greater root mass, length, and area than F. paniculata. Our study,
 by dissociating soil effects from plant effects, demonstrated that plant
 species exert a key control on soil fungi. We suggest that such effects
 may be linked to inter-specific differences in root traits and their
 consequences on nitrogen uptake.
description: fungi_wp2_uniq_mclFasta file containing unic sequences. The cluster number corresponds to MOTU number
DOI: 10.5061/dryad.6mj4t
title: Data from: A novel hearing specialization in the New Zealand bigeye, Pempheris adspersa

description: The New Zealand bigeye, Pempheris adspersa, is a nocturnal planktivore and
 has recently been found to be an active sound producer. The rostral end of
 the swim bladder lies adjacent to Baudelot's ligament which spans
 between the bulla and the cleithrum bone of the pectoral girdle. The aim
 of this study was to use the auditory evoked potential technique to
 physiologically test the possibility that this structure provides an
 enhanced sensitivity to sound pressure in the bigeye. At 100 Hz, bigeye
 had hearing sensitivity similar to that of goldfish (species with a
 mechanical connection between the swim bladder and the inner ear mediated
 by the Weberian ossicles) and were much more sensitive than other teleosts
 without ancillary hearing structures. Severing Baudelot's ligament
 bilaterally resulted in a marked decrease in hearing sensitivity, as did
 swim bladder puncture or lateral line blockage. These results show that
 bigeye have an enhanced sensitivity to sound pressure and provide
 experimental evidence that the functional basis of this sensitivity
 represents a novel hearing specialization in fish involving the swim
 bladder, Baudelot's ligament and the lateral line.
description: Biol Letters
 DataFile contains all raw
 data from auditory evoked potentials as well as all worksheet files
 compiled in TDT BioSig from all Pempheris adspersa manipulations and
 controls.
DOI: 10.5061/dryad.s1s75
title: Data from: A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change

description: Background: Grapes are one of the most economically important fruit crops.
 There are about 60 species in the genus Vitis. The phylogenetic
 relationships among these species are of keen interest for the
 conservation and use of this germplasm. We selected 309 accessions from 48
 Vitis species,varieties, and outgroups, examined ~11 kb (~3.4 Mb total) of
 aligned nuclear DNA sequences from 27 unlinked genes in a phylogenetic
 context, and estimated divergence times based on fossil calibrations.
 Results: Vitis formed a strongly supported clade. There was substantial
 support for species and less for the higher-level groupings (series). As
 estimated from extant taxa, the crown age of Vitis was 28 Ma and the
 divergence of subgenera (Vitis and Muscadinia) occurred at ~18 Ma. Higher
 clades in subgenus Vitis diverged 16 -- 5 Ma with overlapping confidence
 intervals, and ongoing divergence formed extant species at 12 -- 1.3 Ma.
 Several species had species-specific SNPs. NeighborNet analysis showed
 extensive reticulation at the core of subgenus Vitis representing the
 deeper nodes, with extensive reticulation radiating outward. Fitch
 Parsimony identified North America as the origin of the most recent common
 ancestor of extant Vitis species. Conclusions: Phylogenetic patterns
 suggested origination of the genus in North America, fragmentation of an
 ancestral range during the Miocene, formation of extant species in the
 late Miocene-Pleistocene, and differentiation of species in the context of
 Pliocene-Quaternary tectonic and climatic change. Nuclear SNPs effectively
 resolved relationships at and below the species level in grapes and
 rectified several misclassifications of accessions in the repositories.
 Our results challenge current higher-level classifications, reveal the
 abundance of genetic diversity in the genus that is potentially available
 for crop improvement, and provide a valuable resource for species
 delineation, germplasm conservation and use.
description: Vitis phylogeography
 zipVitis
 phylogeography.zip
DOI: 10.5061/dryad.83h07
title: Data from: Scale-dependent foraging ecology of a marine top predator modelled using passive acoustic data

description: 1. Understanding which environmental factors drive foraging preferences is
 critical for the development of effective management measures, but
 resource use patterns may emerge from processes that occur at different
 spatial and temporal scales. Direct observations of foraging are also
 especially challenging in marine predators, but passive acoustic
 techniques provide opportunities to study the behavior of echolocating
 species over a range of scales. 2. We used an extensive passive acoustic
 dataset to investigate the distribution and temporal dynamics of foraging
 in bottlenose dolphins using the Moray Firth (Scotland, UK). Echolocation
 buzzes were identified with a mixture model of detected echolocation
 inter-click intervals, and used as a proxy of foraging activity. A robust
 modelling approach accounting for autocorrelation in the data was then
 used to evaluate which environmental factors were associated with the
 observed dynamics at two different spatial and temporal scales. 3. At a
 broad scale, foraging varied seasonally, and was also affected by sea-bed
 slope and shelf-sea fronts. At a finer scale, we identified variation in
 seasonal use and local interactions with tidal processes. Foraging was
 best predicted at a daily scale, accounting for site-specificity in the
 shape of the estimated relationships. 4. This study demonstrates how
 passive acoustic data can be used to understand foraging ecology in
 echolocating species, and provides a robust analytical procedure for
 describing spatio-temporal patterns. Associations between foraging and
 environmental characteristics varied according to spatial and temporal
 scale, highlighting the need for a multi-scale approach. Our results
 indicate that dolphins respond to coarser-scale temporal dynamics, but
 have a detailed understanding of finer-scale spatial distribution of
 resources.
description: Hourly occurrence of
 bottlenose dolphins' foraging buzzes in POD data from the Moray
 Firth, ScotlandThe data were collected
 using T-PODs and C-PODs (www.chelonia.co.uk). The foraging buzzes were
 identified in the echolocation time series using a Gaussian mixture model.
 For each hourly record, if a buzz was present the value for
 "pres.buzzes" is equal to 1. For each record, the values of the
 available covariates are also provided. The column "id.gees"
 indicates the blocking factor used for GEEs.Hourly_data.csvDaily occurrence of bottlenose dolphins' foraging buzzes in POD data from the Moray Firth, ScotlandThe data were collected using T-PODs and C-PODs (www.chelonia.co.uk). The foraging buzzes were identified in the echolocation time series using a Gaussian mixture model. For each daily record, if a buzz was present the value for "presdaily.buzzes" is equal to 1. For each record, the values of the available covariates are also provided. The column "id.gees" indicates the blocking factor used for GEEs.Daily_data.csv
DOI: 10.5061/dryad.33kn3
title: Data from: A biogeographical regionalisation of Australian Acacia species

description: Aim: To develop a biogeographical regionalization of Australian Acacia
 species and to investigate their environmental correlates. Location:
 Australia. Methods: We used a previously published framework for
 delineating biogeographical regions. We calculated species turnover
 patterns of 1020 Australian Acacia species with distributions estimated
 from 171,758 georeferenced herbarium records aggregated to 100 km × 100 km
 cells (868 across Australia). An agglomerative cluster analysis using a
 matrix of pairwise Simpson's beta (βsim) dissimilarity values was
 applied. Eleven environmental variables at the same resolution as the
 aggregated herbarium records were used to explore the correlates of the
 βsim patterns using a non-metric multidimensional scaling (NMDS) analysis.
 We also used an ANOVA to test the significance of the environmental
 changes between each pair of biogeographical regions. Results: Five major
 Acacia biogeographical regions were proposed. These bioregions were
 broadly similar to the biomes of Australia. A new subdivision of the
 Eremaean biome was proposed for Acacia. The most influential environmental
 variables for the individual bioregions were: (1) temperature seasonality
 and topographic flatness for the south-western temperate bioregion; (2)
 precipitation during the coldest quarter of the year for the south-eastern
 temperate bioregion; (3) annual precipitation, annual mean temperature and
 precipitation seasonality for the monsoonal bioregion; and (4) percentage
 of sand in the top 30 cm of the soil, rock grain size, annual mean
 radiation and annual mean temperature for the Eremaean south and north
 regions. The NMDS analysis provided support for the observed
 biogeographical patterns. The statistical test showed a highly significant
 difference between the environments of the proposed bioregions. Climatic
 variables were consistent predictors across regions, whereas the influence
 of soils and topographic features varied among bioregions. Main
 conclusions: The major Acacia biogeographical regions correspond well to
 historical bioregionalizations, suggesting that the environmental drivers
 of diversification in Acacia are broadly similar to those that act on the
 flora as a whole. Climate seasonality combined with annual values and
 non-climatic factors provide support for the proposed biogeographical
 regionalization for Acacia.
description: Point distribution for
 Australian Acacia speciesSource: Australia's
 Virtual Herbarium. 170,000 digitissed records of Acacia species
 distributions, Australia.1_Point_distribution_Australian_Acacia_species.csvGridded data matrix Australian Acacia species turnoverMatrix based on presence records of 1,020 species of Acacia created in software Biodiverse 0.18.2_Gridded_data_matrix_Australian_Acacia_species_turnover.csv