cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sh553
title: Data from: Phylogeography, historical demography, and habitat suitability modelling of freshwater fishes inhabiting seasonally fluctuating Mediterranean river systems: a case study using the Iberian cyprinid Squalius valentinus

description: The Mediterranean freshwater fish fauna has evolved under constraints
 imposed by the seasonal weather/hydrological patterns that define the
 Mediterranean climate. These conditions have influenced the genetic and
 demographic structure of aquatic communities since their origins in the
 Mid-Pliocene. Freshwater species in Mediterranean-type climates will
 likely constitute genetically well-differentiated populations, to varying
 extents depending on basin size, as a consequence of fragmentation
 resulting from drought/flood cycles. We developed an integrative framework
 to study the spatial patterns in genetic diversity, demographic trends,
 habitat suitability modelling and landscape genetics, to evaluate the
 evolutionary response of Mediterranean-type freshwater fish to seasonal
 fluctuations in weather. To test this evolutionary response, the model
 species used was Squalius valentinus, an endemic cyprinid of the Spanish
 Levantine area, where seasonal weather fluctuations are extreme, although
 our findings may be extrapolated to other Mediterranean-type species. Our
 results underscore the significant role of the Mediterranean climate,
 along with Pleistocene glaciations, in diversification of S. valentinus.
 We found higher nuclear diversity in larger drainage basins, but higher
 mitochondrial diversity correlated to habitat suitability rather than
 basin size. We also found strong correlation between genetic structure and
 climatic factors associated with Mediterranean seasonality. Demographic
 and migration analyses suggested population expansion during glacial
 periods that also contributed to the current genetic structure of S.
 valentinus populations. The inferred models support the significant
 contribution of precipitation and temperature to S. valentinus habitat
 suitability and allow recognizing areas of habitat stability. We highlight
 the importance of stable habitat conditions, fostered by typical karstic
 springs found on the Mediterranean littoral coasts, for the preservation
 of freshwater species inhabiting seasonally fluctuating river systems.
description: Svalentinus_alingmentsAlignments of cytochrome b and RAG 1 sequences in fasta format. Both genes are in the same file, one after the otherSvalentinus_alingment.fas
DOI: 10.5061/dryad.8849
title: Data from: Single nucleotide polymorphisms across a species' range: implications for conservation studies of Pacific salmon

description: Studies of the oceanic and near-shore distributions of Pacific salmon,
 whose migrations typically span thousands of kilometers, have become
 increasingly valuable in the presence of climate change, increasing
 hatchery production, and potentially high rates of bycatch in offshore
 fisheries. Genetics data offer considerable insights into both the
 migratory routes as well as the evolutionary histories of the species.
 However, these types of studies require extensive datasets from spawning
 populations originating from across the species? range. Single nucleotide
 polymorphisms (SNPs) have been particularly amenable for multi-national
 applications because they are easily shared, require little
 inter-laboratory standardization, and can be assayed through increasingly
 efficient technologies. Here we discuss the development of a dataset for
 114 populations of chum salmon through a collaboration among North
 American and Asian researchers, termed PacSNP. PacSNP is focused on
 developing the database and applying it to problems of international
 interest. A dataset spanning the entire range of species provides a unique
 opportunity to examine patterns of variability, and we review issues
 associated with SNP development. We found evidence of ascertainment bias
 within the dataset, variable linkage relationships between SNPs associated
 with ancestral groupings, and outlier loci with alleles associated with
 latitude.
description: PacSNP chum data for
 MERThe file is formatted
 for GenAlEx software, but can easily be converted to Genepop or similar
 formats. Genotypes are in two-column format with missing data designated
 with a “0”. Population code and locus code worksheets follow the rawdata.
 The population order differs between the rawdata which is in numeric order
 and Table 1 of the manuscript which is ordered geographically. This is
 particularly noticeable in the order of the Western Alaska populations
 including the Yukon River. The rawdata includes laboratory names for the
 SNPs; a key to published names is in the locus code worksheet. The mtDNA
 SNPs are listed independently and have not been combined into composite
 haplotypes.
DOI: 10.6084/m9.figshare.31158355.v1
title: GLADE: Accurate inference of <b>G</b>ains, <b>L</b>osses, <b>A</b>ncestral genomes, and <b>D</b>uplication <b>E</b>vents for comparative genomics

description: GLADE: Accurate inference of <b>G</b>ains, <b>L</b>osses, <b>A</b>ncestral genomes, and <b>D</b>uplication <b>E</b>vents for comparative genomics
DOI: 10.18112/openneuro.ds006444.v1.0.8
title: Benchmarking the Impact of Anatomical Segmentation on In Vivo Magnetic Resonance Spectroscopy
DOI: 10.5061/dryad.3948r
title: Data from: Snake venoms are integrated systems, but abundant venom proteins evolve more rapidly

description: Background: While many studies have shown that extracellular proteins
 evolve rapidly, how selection acts on them remains poorly understood. We
 used snake venoms to understand the interaction between ecology,
 expression level, and evolutionary rate in secreted protein systems.
 Venomous snakes employ well-integrated systems of proteins and organic
 constituents to immobilize prey. Venoms are generally optimized to subdue
 preferred prey more effectively than non-prey, and many venom protein
 families manifest positive selection and rapid gene family
 diversification. Although previous studies have illuminated how individual
 venom protein families evolve, how selection acts on venoms as integrated
 systems, is unknown. Results: Using next-generation transcriptome
 sequencing and mass spectrometry, we examined microevolution in two
 pitvipers, allopatrically separated for at least 1.6 million years, and
 their hybrids. Transcriptomes of parental species had generally similar
 compositions in regard to protein families, but for a given protein
 family, the homologs present and concentrations thereof sometimes differed
 dramatically. For instance, a phospholipase A 2 transcript comprising 73.4
 % of the Protobothrops elegans transcriptome, was barely present in the P.
 flavoviridis transcriptome (&lt;0.05 %). Hybrids produced most
 proteins found in both parental venoms. Protein evolutionary rates were
 positively correlated with transcriptomic and proteomic abundances, and
 the most abundant proteins showed positive selection. This pattern holds
 with the addition of four other published crotaline transcriptomes, from
 two more genera, and also for the recently published king cobra genome,
 suggesting that rapid evolution of abundant proteins may be generally true
 for snake venoms. Looking more broadly at Protobothrops, we show that
 rapid evolution of the most abundant components is due to positive
 selection, suggesting an interplay between abundance and adaptation.
 Conclusions: Given log-scale differences in toxin abundance, which are
 likely correlated with biosynthetic costs, we hypothesize that as a result
 of natural selection, snakes optimize return on energetic investment by
 producing more of venom proteins that increase their fitness. Natural
 selection then acts on the additive genetic variance of these components,
 in proportion to their contributions to overall fitness. Adaptive
 evolution of venoms may occur most rapidly through changes in expression
 levels that alter fitness contributions, and thus the strength of
 selection acting on specific secretome components.
description: SQL database with
 intermediate resultsThis database is to be
 used with the accompanying R script.snake_hybridization_2014-10-09.sql.gzR script with analysis pipelineThis script uses data from the accompanying SQL database.habu hybrid.Rmd
DOI: 10.18167/dvn1/7ytqgq
title: Valorcarn-TETIS: corpus
title: Valorcarn-TETIS : corpus

description: Valorcarn Project (2015-2017) [project supported by GloFoodS program (INRA-Cirad)].
&lt;br&gt;
Mining of scientific documents for identification of process that enables to reduce losses and waste.
description: Collecte manuelle (via le Web) d’un corpus en anglais de 7465 mots : 
Valorcarn_web_corpus‧txt
DOI: 10.5061/dryad.g75nq
title: Data from: Genomic determinants of coral heat tolerance across latitudes

description: As global warming continues, reef-building corals could avoid local
 population declines through “genetic rescue” involving exchange of
 heat-tolerant genotypes across latitudes, but only if latitudinal
 variation in thermal tolerance is heritable. Here, we show an
 up–to–10-fold increase in odds of survival of coral larvae under heat
 stress when their parents come from a warmer lower-latitude location.
 Elevated thermal tolerance was associated with heritable differences in
 expression of oxidative, extracellular, transport, and mitochondrial
 functions that indicated a lack of prior stress. Moreover, two genomic
 regions strongly responded to selection for thermal tolerance in
 interlatitudinal crosses. These results demonstrate that variation in
 coral thermal tolerance across latitudes has a strong genetic basis and
 could serve as raw material for natural selection.
description: Linkage map data for
 Acropora millepora2bRAD-based linkage map
 dataAmillepora_linkageMapData_dixon2015.txttag-based RNAseq counts of larval familiesThe samples names identify the cross: first letter- dam, second letted - sire, number - culture replicate. The parents (from A to D) are the same as used for the heat stress experiment (see another tag-seq dataset). The parents A and B are from Orpheus Island (Central GBR), parents C and D are from Princess Charlotte Bay (Northern GBR). The annotations for the genes ("isogroups") are in the transcriptome bundle included with this submission.dixon15_tagSeq_larvalCounts.txttag-based RNAseq counts for heat stress experiment in adult coralsResponse of adult corals to heat stress. Letter identifies a coral colony, numbers 1 to 3 are controls fragments (ambient temperature, 28C), numbers 4 to 6 are heat-stressed fragments (3 days at 31.5C). Colonies A and B are from Orpheus Island (Central GBR), colonies C and D are from Princess Charlotte Bay (Northern GBR). These corals are the same as used as parents to produce larval cohorts (see another tag-seq dataset). The annotations for the genes ("isogroups") are in the transcriptome bundle included with this submission.dixon15_tagSeq_adultCounts.txtSurvival of coral larvae at 35.5CThe table contains counts of larvae surviving after a certain time at 35.5C, out of the initial number of 20 (the only exception is family AB replicate 2, which started with 40 larvae). The parental colonies (A through D) are the same as used for heat stress experiment (see tag-seq data set for heat stress in adults). Colonies A and B are from the Orpheus Island, colonies C and D are from Princess Charlotte Bay. Time is in hours.dixon15_larvalHeatSurvival.csvA.millepora transcriptome sequences and annotationsThis transcriptome was published previously by Moya et al Mol. Ecol. 21, 2440–2454 (2012) and re-annotated for Dixon et al Science 2015 publication.Amillepora_transcriptome_annotations_dixon2015.zip
DOI: 10.5061/dryad.47bm8
title: Data from: Tragopogon turcicus sp. nov. (Asteraceae) from Turkey and its phylogenetic position

description: Tragopogon turcicus Coşkunç., M.Gultepe & Makbul, a new diploid
 species (2n = 2x = 12), is described and illustrated from Kızıldağ
 National Park (Isparta), southwest Anatolia. It is morphologically similar
 to T. oligolepis Hartvig & Strid which is also endemic to Turkey.
 Diagnostic characters, description, conservation status together with
 micro- and macro-morphological properties of achenes and pollen grains are
 given. A phylogenetic analysis based on nrDNA ITS sequence data indicated
 that T. oligolepis is the sister species of the new taxon.
description: morphologic comparision
 of the T. turcica with related speciesTable
 1.docxFigure
 1habit and holotype of
 Tragopogon turcicus
DOI: 10.5061/dryad.8861
title: Data from: Understanding patch departure rules for large carnivores: lion movements support a patch-disturbance hypothesis

description: We test two hypotheses that could account for patch departure by large
 mammalian carnivores. One hypothesis is the unsuccessful hunt hypothesis,
 where carnivores leave an area after an unsuccessful hunt but continue
 hunting in the same area after a successful hunt. The second hypothesis is
 the patch disturbance hypothesis, where carnivores depart the area after a
 successful hunt because of behavioral responses of prey to predator
 presence. We used GPS-collars to monitor the movements of African lions
 (Panthera leo) and identified their kill sites to distinguish between
 these two hypotheses. Lions moved to a different area (&gt;5 km) after
 87 percent of the kills, which supports the patch disturbance hypothesis
 for patch departure behavior of large mammalian carnivores.
description: Data trajectories after
 a killThese data describe the
 movements of 8 lions after some identified kills. Data are from
 GPS-collars.Data random
 trajectoriesThese data correspond to
 48-hour trajectories after a random location that did not correspond to a
 kill site. There are data from the same 8 GPS-collared lions monitored for
 trajectories after a kill.
DOI: 10.5061/dryad.846qk
title: Data from: Mating with an allopatric male triggers immune response and decreases longevity of ant queens

description: In species with lifelong pair bonding, the reproductive interests of the
 mating partners are aligned, and males and females are expected to jointly
 maximize their reproductive success. Mating increases both longevity and
 fecundity of female reproductives (queens) of the ant Cardiocondyla
 obscurior, indicating a tight co-evolution of mating partners. Here, we
 show that mating with a male from their own population increases lifespan
 and reproductive success of queens more than mating with a male from a
 different population, with whom they could not co-evolve. A comparison of
 transcriptomes revealed an increased expression of genes involved in
 immunity processes in queens, which mated with males from a different
 population. Increased immune response might be proximately associated with
 decreased lifespan. Our study suggests a synergistic co-evolution between
 the sexes and sheds light on the proximate mechanisms underlying the
 decreased fitness of allopatrically mated queens.
description: rawdata_htseq_DEseqRohdaten_htseq_DEseq2-2.xlsxWolbachia_wsp_Alignment_Alex_wsp_Alignment_final.fastafitness_data_queensfitness_data.xlsx
DOI: 10.5061/dryad.7nd42
title: Data from: Molecular phylogeny of the subfamily Stevardiinae Gill, 1858 (Characiformes: Characidae): classification and the evolution of reproductive traits

description: Background The subfamily Stevardiinae is a diverse and widely distributed
 clade of freshwater fishes from South and Central America, commonly known
 as “tetras” (Characidae). The group was named “clade A” when first
 proposed as a monophyletic unit of Characidae and later designated as a
 subfamily. Stevardiinae includes 48 genera and around 310 valid species
 with many species presenting inseminating reproductive strategy. No global
 hypothesis of relationships is available for this group and currently many
 genera are listed as incertae sedis or are suspected to be
 non-monophyletic. Results We present a molecular phylogeny with the
 largest number of stevardiine species analyzed so far, including 355
 samples representing 153 putative species distributed in 32 genera, to
 test the group’s monophyly and internal relationships. The phylogeny was
 inferred using DNA sequence data from seven gene fragments (mtDNA: 12S,
 16S and COI; nuclear: RAG1, RAG2, MYH6 and PTR). The results support the
 Stevardiinae as a monophyletic group and a detailed hypothesis of the
 internal relationships for this subfamily. Conclusions A revised
 classification based on the molecular phylogeny is proposed that includes
 seven tribes and also defines monophyletic genera, including a resurrected
 genus Eretmobrycon, and new definitions for Diapoma, Hemibrycon,
 Bryconamericus sensu stricto, and Knodus sensu stricto, placing some small
 genera as junior synonyms. Inseminating species are distributed in several
 clades suggesting that reproductive strategy is evolutionarily labile in
 this group of fishes.
description: Stevardiinae
 concatenated alignmentConcatenated alignment
 with all sequences generated to reconstruct the phylogeny of Stevardiinae.
 The gene partitions are: myh6 = 1 - 621; ptr = 622 - 1158; rag1 = 1159 -
 2520; rag2 = 2521 - 3291; coi = 3292 - 3813; 16s = 3814 - 4387; 12s = 4388
 - 4816. Also, all taxa listed are identified by its name and voucher
 number.Stevardiinae_align.phyStevardiinae treesStevardiinae phylogenies reconstructed with the software's: RAxML (concatenated and gene trees), Garli, STAR and TNT. Trees were rooted in Serrasalmus sp. and bootstraps support are shown when available.Stevardiinae_trees.zip
DOI: 10.5061/dryad.pr10g
title: Data from: Estimating effective population size of guanacos in Patagonia: an integrative approach for wildlife conservation

description: By the mid-1900s the guanaco (Lama guanicoe) approached extinction in
 southern South America due to habitat destruction and hunting. In order to
 maintain the ecological prominence of this iconic species, as well as
 assist in the management of populations that are emerging economically
 while increasing in conservation value, accurate and potentially rapid
 estimates of effective population size (Ne) (demographic and/or genetic)
 are essential. Estimates of Ne generally focus on the genetic effective
 population size; however, we posited that both parameters may be necessary
 to provide more accurate and timely estimates. Therefore, we examined the
 performance of three demographic and four genetic estimators of Ne of
 guanacos in Torres del Paine National Park, Chile, at different years and
 time intervals between 1987 and 1997. We compared our estimates with
 census estimates of the adult population size (Nac) during the same time
 period. Average Ne/Nac ratios of demographic estimates varied between 0.04
 and 0.99 of the adult census size. Genetic estimates varied between 0.02
 and 0.08 of the adult census size. Based upon group composition and
 population size (n = 82) of guanacos in 1975, the number of breeding
 adults was 44 animals. Mean Ne of the single-sample and temporal genetic
 estimators was 43.1, and 34.3, respectively; estimated Ne of one of the
 demographic estimators was 41. Our findings suggest that intermittent
 genetic estimates of Ne (via fecal samples, carcasses, blood collection
 during capture, and/or other non-invasive methods) can provide crucial
 information regarding the genetic integrity of increasingly isolated
 populations of wild South American camelids. Considering the overall
 performance of these estimators, and differences in how each functions, we
 recommend an integrative approach using both genetic and demographic
 estimators, to evaluate Ne for the wild South American camelids and other
 species with polygynous mating systems.
description: Simulations runner:
 software for simulation and analysis of Ne using programs LDNe, MNe,
 ONeSAMP, and TM3.1These files enable the
 user to run simulations. Click on "Simulations" and the program
 opens and is ready to use. Consult the User's Guide for more specific
 questions. The example input can be modified according to the # of loci
 and allele frequencies of the user's data.Simulations
 2015-05-16.zip
DOI: 10.5061/dryad.566h9
title: Data from: More than one way to evolve a weed: Parallel evolution of U.S. weedy rice through independent genetic mechanisms

description: Many different crop species were selected for a common suite of
 ‘domestication traits’, which facilitates their use for studies of
 parallel evolution. Within domesticated rice (Oryza sativa), there has
 also been independent evolution of weedy strains from different cultivated
 varieties. This makes it possible to examine the genetic basis of parallel
 weed evolution and the extent to which this process occurs through shared
 genetic mechanisms. We performed comparative QTL mapping of weediness
 traits using two recombinant inbred line populations derived from crosses
 between an indica crop variety and representatives of each of the two
 independently evolved weed strains found in US rice fields, strawhull (S)
 and blackhull awned (B). Genotyping-by-sequencing provided dense marker
 coverage for linkage map construction (average marker interval
 &lt;0.25 cM), with 6016 and 13 730 SNPs mapped in F5 lines of the S
 and B populations, respectively. For some weediness traits (awn length,
 hull pigmentation and pericarp pigmentation), QTL mapping and sequencing
 of underlying candidate genes confirmed that trait variation was largely
 attributable to individual loci. However, for more complex quantitative
 traits (including heading date, panicle length and seed shattering), we
 found multiple QTL, with little evidence of shared genetic bases between
 the S and B populations or across previous studies of weedy rice.
 Candidate gene sequencing revealed causal genetic bases for 8 of 27 total
 mapped QTL. Together these findings suggest that despite the genetic
 bottleneck that occurred during rice domestication, there is ample genetic
 variation in this crop to allow agricultural weed evolution through
 multiple genetic mechanisms.
description: emergence date S
 popemergence date S
 popY.g.csvemergence date B popemergence date B popW.g.csvheading date S 2012heading date S 2012Y.h12.csvheading date S 2013heading date S 2013Y.h13.csvheading date B 2012heading date B 2012W.h12.csvheading date B 2013heading date B 2013W.h13.csvpanicle length S 2012panicle length S 2012Y.k12.csvpanicle length S 2013panicle length S 2013Y.k13.csvShattering S 2012Shattering S 2012Y.j12.csvShattering S 2013Shattering S 2013Y.j13.csvShattering B 2012Shattering B 2012W.J12.csvShattering B 2012Shattering B 2012W.j13.csvHull color SHull color SY_Phe_rot_Hull.csvHull color BHull color BW_Phe_rot_Hull.csvawn length B 2012awn length B 2012W.c12_rot_awnlength.csvawn length B 2013awn length B 2013W.c13_rot_awnlength.csvPericarp SPericarp SY_Phe_rot_Pericarp.csvPericarp BPericarp BW_Phe_rot_pericarp.csvhetfilt_ricegbs2_Yf_sdS mapping population SNP raw datahetfilt_ricegbs2_Wf_sdB mapping population raw SNP dataAn1Bh4DTH7DTH8Hd1RcHd3a