cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6q3d110
title: Data from: Facultative oviparity in a viviparous skink (Saiphos equalis)

description: Facultative changes in parity mode (oviparity to viviparity, and vice
 versa) are rare in vertebrates, yet offer fascinating opportunities to
 investigate the role of reproductive lability in parity mode evolution.
 Here we report apparent facultative oviparity by a viviparous female of
 the bimodally reproductive skink Saiphos equalis- the first report of
 different parity modes within a vertebrate clutch. Eggs oviposited
 facultatively possess shell characteristics of both viviparous and
 oviparous S. equalis, demonstrating that egg coverings for viviparous
 embryos are produced by the same machinery as those for oviparous
 individuals. Since selection may act in either direction when viviparity
 has evolved recently, squamate reproductive lability may confer a
 selective advantage. We suggest that facultative oviparity is a viable
 reproductive strategy for S. equalis and that squamate reproductive
 lability is more evolutionarily significant than previously acknowledged.
description: Laird et al. Facultative
 oviparity in a viviparous skinkScanning electron
 microscopy of eggshells and associated morphometricsDryad
 submission_zipped.zip
DOI: 10.5061/dryad.r1t6fj5
title: Data from: Modelling the functional link between movement, feeding activity and condition in a marine predator

description: The ability to quantify animals’ feeding activity and the resulting
 changes in their body condition as they move in the environment is
 fundamental to our understanding of a population’s ecology. We use
 satellite tracking data from northern elephant seals (Mirounga
 angustirostris), paired with simultaneous diving information, to develop a
 Bayesian state-space model that concurrently estimates an individual’s
 location, feeding activity, and changes in condition. The model identifies
 important foraging areas and times, the relative amount of feeding
 occurring therein and thus the different behavioral strategies in which
 the seals engage. The fitness implications of these strategies can be
 assessed by looking at the resulting variation in individuals’ condition,
 which in turn affects the condition and survival of their offspring.
 Therefore, our results shed light on the processes affecting an
 individual’s decision-making as it moves and feeds in the environment. In
 addition, we demonstrate how the model can be used to simulate realistic
 patterns of disturbance at different stages of the trip, and how the
 predicted accumulation of lipid reserves varies as a consequence.
 Particularly, disturbing an animal in periods of high feeding activity or
 shortly after leaving the colony was predicted to have the potential to
 lead to starvation. In contrast, an individual could compensate even for
 very severe disturbance if such disturbance occurred outside the main
 foraging grounds. Our modelling approach is applicable to marine mammal
 species that perform drift dives, and can be extended to other species
 where an individual’s buoyancy can be inferred from its diving behavior.
description: ARGOS_LocationDataThe file contains ARGOS satellite telemetry locations for the 26 elephant seals included in the analysis. Each location is associated with an ARGOS location class (lc).Fat mass estimatesThe file contains the estimates (mean and standard deviation) of fat mass at departure from and arrival to the colony for each individual included in the analysis.Depart_Arrive_FatMass_measurements.csvDiving data and lean massThe file contains the diving data for each individual on each day of the foraging trip: median time spent at the bottom during a dive (Bottom_time), median dive duration (Dive_duration), median descent rate (Descent_rate), median ascent rate (Ascent_rate), total number of dives per day (N_dives), number of drift dives per day (N_Drift_dives) and daily median drift rate (Drift_rate). The lean mass on each day for the two assumed functional forms (Lean_mass_1 and Lean_mass_2) and a variable indicating whether the median drift rate on that day was positive or negative (Indicator) are also included.DivingData_LeanMass.csv
DOI: 10.5061/dryad.8jh08mp
title: Data from: Life-history strategies indicate live-bearing in Nothosaurus (Sauropterygia)

description: In Sauropterygia, a diverse group of Mesozoic marine reptiles, fossil
 evidence of viviparity (live‐bearing) only exists for Pachypleurosauria
 and Plesiosauria, and was assumed to also be the case for nothosaurs.
 Previous studies have successfully applied an extant squamate model to
 sauropterygian life‐history traits. In extant squamates, oviparity and
 viviparity are associated with differences in life‐history trait
 combinations. We establish growth curves for Nothosaurus specimens based
 on their humeral histology. We then analyse life‐history traits derived
 from these curves and compare inferred traits to those of modern squamates
 and pachypleurosaurs to assess their reproduction mode. We show that birth
 to adult size ratios (i.e. birth size divided by the mother's size)
 provide good estimates of clutch sizes in extant squamates and in
 viviparous extinct marine reptiles, but these ratios cannot discriminate
 viviparous and oviparous squamates. Thus, large ratios do not indicate
 viviparity in fossil taxa to which the extant squamate model is
 applicable. Applying differences in birth size, age at maturation, and
 maximum longevity that are observed between extant viviparous and
 oviparous squamates to our Nothosaurus sample, we identified 7 out of 24
 specimens as being potentially viviparous. Conversely, they suggested
 oviparity for many nothosaurs but also for many pachypleurosaur samples.
 Under the assumption that the entire clade Pachypleurosauria was
 viviparous, the majority of nothosaurs would also have been viviparous as
 they comprised trait combinations similar to those seen in
 pachypleurosaurs. Overall, this suggests that within nothosaurs and
 pachypleurosaurs both reproduction modes existed in different taxa.
description: Griebeler_Klein_Supplementary_InformationSupporting Information with growth records of nothosaurs, additional statistical analysis on differences in life-history strategies of extant squamates, a detailed description of our growth curve fitting method, tables with equations fitted to the growth record of nothosaur specimens, and life-history traits inferred from nothosaur growth curves.
DOI: 10.5061/dryad.2kc5rh0
title: Data from: Estimating the relative fitness of escaped farmed salmon offspring in the wild and modeling the consequences of invasion for wild populations

description: Throughout their native range, wild Atlantic salmon populations are
 threatened by hybridization and introgression with escapees from net-pen
 salmon aquaculture. Although domestic-wild hybrid offspring have shown
 reduced fitness in lab and field experiments, consequential impacts on
 population abundance and genetic integrity remain difficult to predict in
 the field, in part because the strength of selection against domestic
 offspring is often unknown and context-dependent. Here we follow a single
 large escape event of farmed Atlantic salmon in southern Newfoundland and
 monitor changes in the in-river proportions of hybrids and feral
 individuals over time using genetically-based hybrid identification. Over
 a three-year period following the escape, the overall proportion of wild
 parr increased consistently (total wild proportion of 71.6%, 75.1%, 87.5%
 each year, respectively), with subsequent declines in feral (genetically
 pure farmed individuals originating from escaped, farmed adults) and
 hybrid parr. We quantify the strength of selection against parr of
 aquaculture ancestry and explore the genetic and demographic consequences
 for populations in the region. Within-cohort changes in the relative
 proportions of feral and F1 parr suggest reduced relative survival
 compared to wild individuals over the first (0.15 and 0.81 for feral and
 F1, respectively), and second years of life (0.26, 0.83). These relative
 survivorship estimates were used to inform an individual-based salmon
 eco-genetic model to project changes in adult abundance and overall allele
 frequency across three invasion scenarios ranging from short-term to
 long-term invasion and three relative survival scenarios. Modeling results
 indicate that total population abundance and time to recovery were greatly
 affected by relative survivorship and predict significant declines in wild
 population abundance under continued large escape events and calculated
 survivorship. Overall this work demonstrates the importance of estimating
 the strength of selection against domestic offspring in the wild to
 predict the long-term impact of farmed salmon escape events on wild
 populations.
description: Genepop_2016samples_allagesGenotypes at 95 selected loci for all samples collected in 2016 from southern Newfoundland (Yoy - Smolt).FieldAges_1516All individuals (age Yoy to 2+) sampled from southern Newfoundland, by age.
DOI: 10.22000/g3b6rp2qk6m4ndf8
title: Dataset for "Photochemical Deracemization of Chromanes and its Application to the Synthesis of Enantiopure Bioactive Compounds"

description: The dataset comprises analytical data for the characterization of the synthesized compounds and computational studies.
DOI: 10.5061/dryad.310pf05
title: Data from: Genome-wide SNP data revealed the extent of linkage disequilibrium, persistence of phase and effective population size in purebred and crossbred buffalo populations

description: Linkage disequilibrium (LD) is a useful parameter for guiding the accuracy
 and power of both genome-wide association studies (GWAS) and genomic
 selection (GS) among different livestock species. The present study
 evaluated the extent of LD, persistence of phase and effective population
 size (Ne) for the purebred (Mediterranean buffalo; n=411) and crossbred
 [Mediterranean × Jianghan × Nili-Ravi buffalo, n=9; Murrah × Nili-Ravi ×
 local (Xilin or Fuzhong) buffalo, n=36] buffalo populations using the 90K
 Buffalo SNP genotyping array. The results showed that the average square
 of correlation coefficient (r2) between adjacent SNP was 0.13 ± 0.19
 across all autosomes for purebred and 0.09 ± 0.13 for crossbred, and the
 most rapid decline in LD was observed over the first 200 kb. Estimated r2
 ≥ 0.2 extended up to approximately 50 kb in crossbred and 170 kb in
 purebred populations, while average r2 values ≥ 0.3 were respectively
 observed in the approximately 10 kb and 60 kb in the crossbred and
 purebred populations. The largest phase correlation (RP,C = 0.47) was
 observed at the distance of 100 kb, suggesting that this phase was not
 actively preserved between the two populations. Estimated Ne for the
 purebred and crossbred population at the current generation was 387 and
 113 individuals, respectively. These findings may provide useful
 information to guide the GS and GWAS in buffaloes.
description: buffalo SNPchip
 dataSNP data used in the LD
 analysis for purebred and crossbred buffalo populations. SNP chip data are
 in binary PLINK format.
DOI: 10.5061/dryad.4k3v0kg
title: Data from: RAD-seq reveals genetic structure of the F2-generation of natural willow hybrids (Salix L.) and a great potential for interspecific introgression

description: Background: Hybridization of species with porous genomes can eventually
 lead to introgression via repeated backcrossing. The potential for
 introgression between species is reflected by the extent of segregation
 distortion in later generation hybrids. Here we studied a population of
 hybrids between Salix purpurea and S. helvetica that has emerged within
 the last 30 years on a glacier forefield in the European Alps due to
 secondary contact of the parental species. We used 5,758 biallelic SNPs
 produced by RAD sequencing with the aim to ascertain the predominance of
 backcrosses (F1 hybrid x parent) or F2 hybrids (F1 hybrid x F1 hybrid)
 among hybrid offspring. Further, the SNPs were used to study segregation
 distortion in the second hybrid generation. Results: The analyses in
 STRUCTURE and NewHybrids revealed that the population consisted of parents
 and F1 hybrids, whereas hybrid offspring consisted mainly of backcrosses
 to either parental species, but also some F2 hybrids. Although there was a
 clear genetic differentiation between S. purpurea and S. helvetica (FST =
 0.24), there was no significant segregation distortion in the backcrosses
 or the F2 hybrids. Plant height of the backcrosses resembled the
 respective parental species, whereas F2 hybrids were more similar to the
 subalpine S. helvetica. Conclusions: The co-occurrence of the parental
 species and the hybrids on the glacier forefield, the high frequency of
 backcrossing, and the low resistance to gene flow via backcrossing make a
 scenario of introgression in this young hybrid population highly likely,
 potentially leading to the transfer of adaptive traits. We further suggest
 that this willow hybrid population may serve as a model for the
 evolutionary processes initiated by recent global warming.
description: STRUCTURE_input_SalixThis file contains the dataset generated for the population genetic analysis of Salix purpurea (Sp1-Sp10), S. helvetica (Sh1-Sh10) and their first (Hybrid1-45) and second generation hybrids (Hyb+nr). The genotype data is arranged in STRUCTURE format. The alleles at the 5758 loci are coded by numbers (1=A, 2=C, 3=G, 4=T). The loci names are arbitrary numbers assigned by STACKS. For more information on the hybrids see also BioProject ID PRJNA429746.
DOI: 10.5061/dryad.4rf13r8
title: Data from: Airflow analysis of Pyeongtaek St. Mary’s Hospital during hospitalization of the First Middle East respiratory syndrome patient in Korea

description: Middle East Respiratory Syndrome (MERS) is known to be transmitted through
 close contact. However, epidemiological surveys of MERS in Korea indicated
 that some secondary patients were infected without close contact.
 Therefore, the possibility of other transmission routes must be
 identified. In this study, the possibility of MERS spreading through
 airflow was investigated on the 8th floor of Pyeongtaek St. Mary's
 Hospital. Computational fluid dynamics was used to analyze the indoor
 airflow and passive tracer diffusion during the index patient’s stay. Six
 cases were simulated for different outdoor wind directions and indoor
 mechanical ventilation operations. When a passive tracer was released in
 ward 8104, where the index patient was hospitalized, the passive tracer
 spread through the indoor airflow, which was created by the outdoor
 airflow. Ward 8109, which had the largest number of infected cases and was
 far distant from ward 8104, showed passive tracer concentration in all
 cases. This result indicates that MERS may have spread through airflow.
 The study results do not imply that the infection pathway of MERS is
 airborne. However, the results show the possibility of MERS spreading
 through airflow in specific environments such as poor ventilation
 environments.
description: Wind profile for West
 windWind profile for West
 windWind porfile for West
 southwest windWind porfile for West
 southwest windPassive tracer
 concentrationPassive tracer
 concentration
DOI: 10.5061/dryad.p1n53q4
title: Data from: Abnormal thalamo-cortical network dynamics in migraine

description: Objective: To investigate the dynamic functional connectivity of
 thalamo-cortical networks in interictal migraine patients and whether
 clinical features are associated with abnormal connectivity. Methods: We
 investigated dynamic functional network connectivity (dFNC) of the
 migraine brain in 89 interictal migraine patients and 70 healthy controls.
 We focused on the temporal properties of thalamocortical connectivity
 using sliding window cross-correlation, clustering state analysis, and
 graph-theory methods. Relationships between clinical symptoms and abnormal
 dFNC were evaluated using a multivariate linear regression model. Results:
 Five dFNC brain states were identified to characterize and compare dynamic
 functional connectivity patterns. We demonstrated that migraineurs spent
 more time in a strongly interconnected between-network state, but they
 spent less time in a sparsely-connected state. Interestingly, we found
 that abnormal posterior thalamus (pulvinar nucleus) dFNC with the visual
 cortex and the precuneus were significantly correlated with headache
 frequency of migraine. Further topological measures revealed migraineurs
 had significantly lower efficiency of information transfer in both global
 and local dFNC. Conclusion: Our results demonstrated a transient
 pathological state with atypical thalamo-cortical connectivity in
 migraineurs and extended current findings regarding abnormal
 thalamo-cortical networks and dysrhythmia in migraine.
description: Supplement
 DataSupplement Data for
 "Abnormal thalamo-cortical network dynamics in
 migraine"Supplementary
 material.docx
DOI: 10.5061/dryad.1v72g43
title: Data from: Prediction of forest aboveground net primary production from high-resolution vertical leaf-area profiles

description: Temperature and precipitation explain about half the variation in
 aboveground net primary production (ANPP) among tropical forest sites, but
 determinants of remaining variation are poorly understood. Here we test
 the hypothesis that the amount of leaf area, and its vertical arrangement,
 predicts ANPP when other variables are held constant. Using measurements
 from airborne lidar in a lowland Neotropical rain forest, we quantify
 vertical leaf-area profiles and develop models of ANPP driven by leaf area
 and other measurements of forest structure. Vertical leaf-area profiles
 predict 38% of the variation among plots. This number is 4.5 times greater
 than models using total leaf area (disregarding vertical arrangement) and
 2.1 times greater than models using canopy height alone. Further, ANPP
 predictions from vertical leaf-area profiles were less biased than
 alternate metrics. Variation in ANPP not attributable to temperature or
 precipitation can be predicted by the vertical distribution of leaf area
 in this system.
description: lidar data for each
 CARBONO field plotLidar data collected at
 La Selva Biological Station, Costa Rica, in September and October 2009
 using the Optech 3100EA sensor. A separate file is included for lidar data
 over each 0.5 ha field plot. Each data file is labeled with the plot ID
 but is not georeferenced to protect the exact location of field
 plots.lidar_files.zip.zipLitter production data for CARBONO plotsBiweekly litterfall data for the CARBONO plot network in La Selva, Costa Rica. Original data and detailed methods are available at www.ots.ac.cr/carbonoproject. Data are day-adjusted values per plot from the 'TOTLITDATA' tab of original data files.Litter.csvTree ID information for trees in CARBONO plotsIndividual tree information for each tree ID in CARBONO plots at La Selva Biological Station, Costa Rica. Original data and detailed methods are available from www.ots.ac.cr/carbonoproject.TreeIDs.csvTree species information for CARBONO plotsTree species code, name, and wood density for the CARBONO plot network in La Selva, Costa Rica. Original data and detailed methods are available at www.ots.ac.cr/carbonoproject.Species.csvWood production data for CARBONO plotsWood production data for the CARBONO plot network in La Selva, Costa Rica. Original data and detailed methods are available at www.ots.ac.cr/carbonoproject.Wood.csvAnnual canopy height measurements for CARBONO plotsAnnual canopy height measurements on a 5 m x 5 m grid in CARBONO plots at La Selva Biological Station, Costa Rica. Original data and detailed methods are available from www.ots.ac.cr/carbonoproject.AnnualCanopyHeight.csv
DOI: 10.5061/dryad.20
title: Data from: Testing for unequal rates of morphological diversification in the absence of a detailed phylogeny: case study from characiform fishes

description: This study develops the random phylogenies rate test (RAPRATE), a
 likelihood method that simulates morphological evolution along randomly
 generated phylogenies, and uses it to determine whether a considerable
 difference in morphological diversity between two sister clades of South
 American fishes should be taken as evidence of differing rates of
 morphological change or lineage turnover. Despite identical ages of
 origin, similar species richness, and sympatric geographic distributions,
 the morphological and ecological diversity of the superfamily Anostomoidea
 exceeds that of the Curimatoidea. The test shows with 90% confidence
 (using variance among species as the measure of morphological diversity)
 or 99% confidence (using volume of occupied morphospace) that the rate of
 morphological change per unit time in the Anostomoidea likely exceeded
 that of the Curimatoidea. Variation in the rate of lineage turnover
 (speciation and extinction rates) is not found to affect greatly the
 morphological diversity of simulated clades and is not a likely
 explanation of the observed difference in morphological diversity in this
 case study. Though a 17% or greater delay in the onset of diversification
 in the Curimatoidea remains a possible alternative explanation of unequal
 morphological diversification, further simulations suggest that two clades
 drawn from the possible treespace of the Anostomoidea and Curimatoidea
 will rarely differ so greatly in the onset of diversification. Several
 uniquely derived morphological and ecological features of the Anostomoidea
 and Curimatoidea may have accelerated or decelerated their rate of
 morphological change, including a marked lengthening of the quadrate that
 may have relaxed structural constraints on the evolution of the anostomoid
 jaw.
description: Morphospace
 SpecimensSpecies, lot numbers and
 numbers of specimens used to create the morphospace. Institutional
 abbreviations are as listed at
 http://www.asih.org/files/codons.pdfEvo_22_Table
 S1.docRelative
 WarpsResults of a relative
 warps analysis done in tpsRelw using the data in
 http://dx.doi.org/10.5061/dryad.20/3. The data in the Excel spreadsheet
 were used to prepare the morphospace figures that appear in Sidlauskas
 2007. The order of taxa in the spreadsheet should match the order of taxa
 in the TPS file.Sidlauskas 2007
 Data.xlsLandmark
 ConsensusesRaw 2D coordinate
 positions representing the geometry of anatomical landmarks taken from the
 skulls of 151 fish species. This is a raw text file. Each entry includes
 the line LM=21 (indicating that there are 21 landmarks per species), a
 list of the 21 landmarks (X and Y coordinates), and an ID line that
 includes the name of the species to which the 21 landmarks _above_ the ID
 belong. The file is intended to be analyzed with the tpsRelw program by F.
 James Rohlf, which is available at
 http://life.bio.sunysb.edu/morph/Sidlauskas 2007 Landmark
 Consensuses.tps