cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.3zntxz
title: Occurrence Download

description: A dataset containing 102316 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is one of (China, Japan, Korea (Democratic People’s Republic of), Korea, Republic of, Pakistan, India, Nepal, Bhutan, Bangladesh, Sri Lanka, Myanmar, Thailand, Lao People’s Democratic Republic, Cambodia, Viet Nam, Chinese Taipei, Philippines, Malaysia, Indonesia, Papua New Guinea, Solomon Islands, Australia, Timor-Leste, Afghanistan)",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Palamocladium leskeoides, Pandanus furcatus, Paramignya monophylla, Parochetus communis, Parthenocissus semicordata, Paspalum conjugatum, Pelekium contortulum, Peperomia heyneana, Persicaria pubescens, Persicaria strigosa, Phaeoceros laevis, Phalaris arundinacea, Philonotis angusta, Philonotis falcata, Philonotis thwaitesii, Philonotis turneriana, Phlegmariurus hamiltonii, Phoebe cathia, Phoebe lanceolata, Pholidota imbricata, Photinia integrifolia, Picris hieracioides, Pilea melastomoides, Pimpinella candolleana, Pinnatella alopecuroides, Pinnatella foreauana, Piper mullesua, Plagiochila nepalensis, Plagiomnium rhynchophorum, Plagiomnium rostratum, Plantago asiatica, Pogonatum microstomum, Pogonatum neesii, Pogonatum perichaetiale, Pogostemon auricularius, Pohlia elongata, Pohlia flexuosa, Polygala arillata, Polygala sibirica, Polystichum squarrosum, Porella campylophylla, Potentilla sundaica, Pothos scandens, Procris crenata, Prunella vulgaris, Prunus ceylanica, Pseudechinolaena polystachya, Pseudocyclosorus tylodes, Pseudognaphalium adnatum, Pseudognaphalium hypoleucum, Pseudophegopteris pyrrhorachis, Pseudopogonatherum quadrinerve, Pterobryopsis orientalis, Ptychomitrium indicum, Pyrrhobryum spiniforme, Pyrrosia porosa, Quercus leucotrichophora, Racopilum orthocarpum, Radula perrottetii, Radula tjibodensis, Ranunculus diffusus, Ranunculus muricatus, Remusatia vivipara, Rhamnus virgata, Rhamnus wightii, Rhodobryum giganteum, Rhododendron arboreum, Rhynchoglossum obliquum, Rochelia zeylanica, Rubus ellipticus, Rubus rugosus, Rumex nepalensis)"
 ]
}

 The dataset includes 102316 records from 498 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000434-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.fg7g4
title: Data from: Linkage mapping of a polymorphic plumage locus associated with intermorph incompatibility in the Gouldian finch (Erythrura gouldiae)

description: Colour polymorphism is known to facilitate speciation but the genetic
 basis of animal pigmentation and how colour polymorphisms contribute to
 speciation is poorly understood. Restricted recombination may promote
 linkage disequilibrium between the colour locus and incompatibility genes.
 Genomic rearrangement and the position of relevant loci within a
 chromosome are important factors that influence the frequency of
 recombination. Therefore, it is important to know the position of the
 colour locus, gene order and recombination landscape of the chromosome to
 understand the mechanism that generates incompatibilities between morphs.
 Recent studies showed remarkable pre- and postzygotic incompatibilities
 between sympatric colour morphs of the Gouldian finch (Erythrura
 gouldiae), in which head feather colour is genetically determined by a
 single sex-linked locus, Red. We constructed a genetic map for the Z
 chromosome of the Gouldian finch (male-specific map distance=131 cM),
 using 618 captive-bred birds and 34 microsatellite markers, to investigate
 the extent of inter- and intraspecific genomic rearrangements and
 variation in recombination rate within the Z chromosome. We refined the
 location of the Red locus to a ~7.2-cM interval in a region with a
 moderate recombination rate but outside the least-recombining, putative
 centromeric region. There was no evidence of chromosome-wide genomic
 rearrangements between the chromosomes carrying the red or black alleles
 with the current marker resolution. This work will contribute to
 identifying the causal gene, which will in turn enable alternative
 explanations for the association between incompatibility and colouration,
 such as fine-scale linkage disequilibrium, genomic rearrangements and
 pleiotropy, to be tested.
description: GouldianFinchMappingData and scripts used in genetic mapping of the Gouldian finch Z chromosome and the Red locus.CriMaker_version1.1CriMaker version1.1: a perl program to make input files for CRI-MAP and check genotype errors.
DOI: 10.5061/dryad.cd0cq
title: Data from: Precocious sexual dimorphism and the Lilliput effect in Neo-Tethyan Ostracoda (Crustacea) through the Permian–Triassic boundary

description: The Elikah River section spanning the Lopingian (Late Permian) to the
 Griesbachian (Early Triassic) time interval in the Central Alborz
 Mountains (north Iran) was sampled for ostracod analysis. We report 79
 species distributed among 38 genera. Four new species are described:
 Acratia? pervagata Forel sp. nov., Microcheilinella alborzella Forel sp.
 nov., Basslerella superarella Crasquin sp. nov. and Cavellina nesenensis
 Crasquin sp. nov. The ontogeny of 13 species is described and sexual
 dimorphism in the genus Microcheilinella is here undoubtedly recognized
 for the first time. Six species show precocious sexual dimorphism of their
 carapace as early as A-5 juvenile. The Lilliput effect is for the first
 time recorded and quantified for two species. Rare long-time span
 Palaeocopida species, known throughout the entire Permian, document
 relatively long-term evolution, including the size and growth rate
 modifications associated with the earlier appearance of carapace sexual
 dimorphism through time. These patterns might be related to the
 Guadalupian–Lopingian events and/or to climatic modifications occurring
 during the Permian interval.
description: Foreletal. APPENDIX
 1Stratigraphical log,
 samples positions and distribution of the ostracods species through the
 productive portion of the Elikah river section, Alborz, Iran. W.:
 Wuchiapingian stage, Jul.: occurrence of the conodont Hindeodus julfensis,
 par.: occurrence of the conodont Hindeodus parvus (PTB: red line).
 Brachiopods bizones: P. ova.: Permophricodothyris ovata Biozone, E. lat.:
 Enteletes lateroplicatus Biozone (Angiolini et al.
 2010).Foreletal. APPENDIX
 2Abundance and
 occurrences of the cf. and open nomenclature ostracod species from the
 Permian-Triassic transition of the Elikah river section
 (Iran).
DOI: 10.5061/dryad.d6299fr
title: Data from: Complex data produce better characters

description: Two studies were conducted to explore the use of complex data in character
 description and hybrid identification. In order to determine if complex
 data allow the production of better characters, eight groups of plant
 systematists were given two classes of drawings of plant parts, and asked
 to divide them into character states (clusters) in two separate
 experiments. The first class of drawings consisted only of cotyledons. The
 second class consisted of triplets of drawings: a cotyledon, seedling
 leaf, and inflorescence bract. The triplets were used to simulate complex
 data such as might be garnered by looking at a plant. Each experiment
 resulted in four characters (groups of clusters), one for each group of
 systematists. Visual and statistical analysis of the data showed that the
 systematists were able to produce smaller, more precisely defined
 character states using the more complex drawings. The character states
 created with the complex drawings also were more consistent across
 systematists, and agreed more closely with an independent assessment of
 phylogeny. To investigate the utility of complex data in an applied task,
 four observers rated 250 hybrids of Dubautia ciliolata X arborea based on
 the overall form (Gestalt) of the plants, and took measurements of a
 number of features of the same plants. A composite score of the
 measurements was created using principal components analysis. The
 correlation between the scores on the first principal component and the
 Gestalt ratings was computed. The Gestalt ratings and PC scores were
 significantly correlated, demonstrating that assessments of overall
 similarity can be as useful as more conventional approaches in determining
 the hybrid status of plants.
description: Appendix
 1Kirchoff_Appendix_1.htmlAppendix 2Kirchoff_Appendix_2.html
DOI: 10.5061/dryad.m6079
title: Data from: Optimum design of family structure and allocation of resources in association mapping with lines from multiple crosses

description: Family mapping is based on multiple segregating families and is becoming
 increasingly popular due to advantages over population mapping. Though
 much progress has been made recently, the optimum design and allocation of
 resources for family mapping remains unclear. Here, we addressed these
 issues using a simulation study, resample model averaging and
 cross-validation approaches. Our results show that in family mapping, the
 predictive power and the accuracy of QTL detection depend greatly on the
 population size and phenotyping intensity. With small population sizes or
 few test environments, QTL results become unreliable and are hampered by a
 large bias in the estimation of the proportion of genotypic variance
 explained by the detected QTL. In addition, we observed that even though
 quality results can be achieved with low marker densities, no plateau is
 reached with our full marker complement. This suggests that higher quality
 results could be achieved with greater mar ker densities or sequence data,
 which will be available in the near future for many species.
description: Liu_et_al_BLUEsDataPhenotypic data (BLUEs) underlying the QTL analysisLiu_et_al_MarkerDataGenotypic data underlying the QTL sudyLiu_et_al_SimulationSimulation study
DOI: 10.5061/dryad.gb125
title: Data from: Quality control processes in allografting: a twenty-year retrospective review of a hospital-based bone bank in Taiwan

description: Musculoskeletal allografts are now commonly used. To decrease the
 potential risks of transmission of pathogenic bacteria, fungi, or viruses
 to the transplant recipients, certain issues regarding the management of
 patients who receive contaminated allografts need to be addressed. We
 aimed to clarify the incidence and extent of disease transmission from
 allografts by analyzing the allografting procedures performed in the bone
 bank of our hospital over the past 20 years. We retrospectively reviewed
 the data from our allograft registry center on 3979 allografts that were
 implanted in 3193 recipients throughout a period of two decades, from July
 1991 to June 2011. The source of the allografts, results of all screening
 tests, dates of harvesting and implantation, and recipients of all
 allografts were checked. With the help of the Center for Infection Control
 of our hospital, a strict prospective, hospital-wide, on-site surveillance
 was conducted, and every patient with healthcare-associated infection was
 identified. Fisher’s exact test was used to compare the infection rate
 between recipients with sterile allografts and those with contaminated
 allografts. The overall discard and infection rates were, respectively,
 23% and 1.3% in the first decade (1991–2001); and 18.4% and 1.25% in the
 second decade (2001–2011). The infection rate of contaminated allograft
 recipients was significantly higher than that of sterile allograft
 recipients (10% vs. 1.15%, P &lt; 0.01) in the second decade. Both
 infection and discard rates of our bone bank are comparable with those of
 international bone banks. Strict allograft processing and adequate
 prophylactic use of antibiotics are critical to prevent infection and
 disease transmission in such cases.
description: 20-year bone bank
 dataThese data contains the
 information of donors, recipient, and the lab data
 results.supplemental file
 revised.xls
DOI: 10.5061/dryad.8rq62
title: Data from: Anomalous unrooted gene trees

description: The coalescent and multispecies coalescent model rooted genealogies
 backward through time. Often, the direction of time is unknown in trees
 estimated from molecular sequences due to reversible mutation models,
 absence of an appropriate outgroup, and the absence of the molecular
 clock. In this paper, probabilities of unrooted gene-tree topologies under
 the multispecies coalescent are considered. The main result is that for
 any species-tree topology with 7 or more taxa, there exist branch lengths
 such that there are unrooted gene-tree topologies that are more likely
 than the one that has the same unrooted topology as the species tree.
 Species trees with such anomalous unrooted gene trees (AUGTs) are
 characterized for trees with 5 and 6 taxa, and patterns of branch lengths
 leading to AUGTs and rooted anomalous gene trees (AGTs) are explored. The
 results could be useful for understanding gene tree discordance and for
 designing simulations studies for inferring challenging species trees.
description: AUGTsupplementIncludes version of COAL used to compute gene tree probabilities symbolically and numerically to find AUGTs, and files to find enumerations of topologies and equivalence classes of rooted topologies with the same unrooted topology.
DOI: 10.5061/dryad.68mc8
title: Data from: Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing

description: High-throughput sequencing has been proposed as a method to genotype
 microsatellites and overcome the four main technical drawbacks of
 capillary electrophoresis: amplification artifacts, imprecise sizing,
 length homoplasy, and limited multiplex capability. The objective of this
 project was to test a high-throughput amplicon sequencing approach to
 fragment analysis of short tandem repeats and characterize its advantages
 and disadvantages against traditional capillary electrophoresis. We
 amplified and sequenced 12 muskrat microsatellite loci from 180 muskrat
 specimens and analyzed the sequencing data for precision of allele
 calling, propensity for amplification or sequencing artifacts, and for
 evidence of length homoplasy. Of the 294 total alleles, we detected by
 sequencing, only 164 alleles would have been detected by capillary
 electrophoresis as the remaining 130 alleles (44%) would have been hidden
 by length homoplasy. The ability to detect a greater number of unique
 alleles resulted in the ability to resolve greater population genetic
 structure. The primary advantages of fragment analysis by sequencing are
 the ability to precisely size fragments, resolve length homoplasy,
 multiplex many individuals and many loci into a single high-throughput
 run, and compare data across projects and across laboratories (present and
 future) with minimal technical calibration. A significant disadvantage of
 fragment analysis by sequencing is that the method is only practical and
 cost-effective when performed on batches of several hundred samples with
 multiple loci. Future work is needed to optimize throughput while
 minimizing costs and to update existing microsatellite allele calling and
 analysis programs to accommodate sequence-aware microsatellite data.
description: digital Fragment
 Analysis HistogramsHistograms (in text
 files) of each microsatellite locus from Ondatra zibethicus (muskrat).
 These histograms were created with a custom Python script from Illumina
 MiSeq paired-end sequencing reads that were merged, quality filtered, and
 de-replicated. A file to map the sample to the specimen ID (and its
 sampling population) is in the ReadMe file.OzHistograms.zipdigital Fragment Analysis Final GenotypesFinal microsatellite genotypes for each muskrat specimen, including muskrat ID, location, allele (0,1), and eleven micorsatellite loci. A text file that maps alleles to their sequence is in the ReadMe file.finalGenotypes.txt
DOI: 10.5061/dryad.4cg84
title: Data from: Effects of the demographic transition on the genetic variances and covariances of human life history traits

description: The recent demographic transitions to lower mortality and fertility rates
 in most human societies have led to changes and even quick reversals in
 phenotypic selection pressures. This can only result in evolutionary
 change if the affected traits are heritable, but changes in environmental
 conditions may also lead to subsequent changes in the genetic variance and
 covariance (the G matrix) of traits. It currently remains unclear if there
 have been concomitant changes in the G matrix of life history traits
 following the demographic transition. Using 300 years of genealogical data
 from Finland, we found that four key life history traits were heritable
 both before and after the demographic transition. The estimated
 heritabilities allow a quantifiable genetic response to selection during
 both time periods, thus facilitating continued evolutionary change.
 Further, the G matrices remained largely stable but revealed a trend for
 an increased additive genetic variance and thus evolutionary potential of
 the population after the transition. Our results demonstrate the validity
 of predictions of evolutionary change in human populations even after the
 recent dramatic environmental change, and facilitate predictions of how
 our biology interacts with changing environments, with implications for
 global public health and demography.
description: Bolund et al.
 DATAExcel file containing
 data used for "Effects of the demographic transition on the genetic
 variances and covariances of human life history traits". Full data is
 given for individuals born more than 100 years prior to the end of data
 collection. Summary data only is provided for individuals born in the last
 100 years. Summaries of G and P matrices are provided for all time
 periods. For further information, see the ReadMe file.BolundetalDATAandTABLES.xlsx
DOI: 10.5061/dryad.g042c
title: Data from: MHC-mediated spatial distribution in brown trout (Salmo trutta) fry

description: Major histocompatibility complex (MHC) class I-linked microsatellite data
 and parental assignment data for a group of wild brown trout (Salmo trutta
 L.) provide evidence of closer spatial aggregation among fry sharing
 greater numbers of MHC class I alleles under natural conditions. This
 result confirms predictions from laboratory experiments demonstrating a
 hierarchical preference for association of fry sharing MHC alleles.
 Full-siblings emerge from the same nest (redd), and a passive kin
 association pattern arising from limited dispersal from the nest (redd
 effect) would predict that all such pairs would have a similar
 distribution. However, this study demonstrates a strong, significant trend
 for reduced distance between pairs of full-sibling fry sharing more MHC
 class I alleles reflecting their closer aggregation (no alleles shared,
 311.5±(s.e.)21.03m; one allele shared, 222.2±14.49m; two alleles shared,
 124.9±23.88m; P&lt;0.0001). A significant trend for closer aggregation
 among fry sharing more MHC class I alleles was also observed in fry pairs,
 which were known to have different mothers and were otherwise unrelated
 (ML-r=0) (no alleles: 457.6±3.58m; one allele (422.4±3.86 m); two alleles
 (381.7±10.72 m); P&lt;0.0001). These pairs are expected to have
 emerged from different redds and a passive association would then be
 unlikely. These data suggest that sharing MHC class I alleles has a role
 in maintaining kin association among full-siblings after emergence. This
 study demonstrates a pattern consistent with MHC-mediated kin association
 in the wild for the first time.
description: FryDataUsed
DOI: 10.5061/dryad.sj8vk
title: Data from: Herbivory promotes dental disparification and macroevolutionary dynamics in grunters (Teleostei: Terapontidae), a freshwater adaptive radiation

description: Trophic shifts into new adaptive zones have played major (although often
 conflicting) roles in reshaping the evolutionary trajectories of many
 lineages. We analyze data on diet, tooth, and oral morphology and relate
 these traits to phenotypic disparification and lineage diversification
 rates across the ecologically diverse Terapontidae, a family of
 Australasian fishes. In contrast to carnivores and most omnivores, which
 have retained relatively simple, ancestral caniniform tooth shapes,
 herbivorous terapontids appear to have evolved a variety of novel tooth
 shapes at significantly faster rates to meet the demands of plant-based
 diets. The evolution of herbivory prompted major disparification,
 significantly expanding the terapontid adaptive phenotypic continuum into
 an entirely novel functional morphospace. There was minimal support for
 our hypothesis of faster overall rates of integrated tooth shape, spacing,
 and jaw biomechanical evolution in herbivorous terapontids in their
 entirety, compared with other trophic strategies. There was, however,
 considerable support for accelerated disparification within a diverse
 freshwater clade containing a range of specialized freshwater herbivores.
 While the evolutionary transition to herbivorous diets has played a
 central role in terapontid phenotypic diversification by pushing
 herbivores toward novel fitness peaks, there was little support for
 herbivory driving significantly higher lineage diversification compared
 with background rates across the family.
description: Maximum clade
 credibility tree for the terapontid phylogenyMaximum clade
 credibility tree for the terapontid phylogeny (nexus
 format)Terapontidae_CON_TREE.tre500 BEAST generated trees500 BEAST generated trees for Terapontidae (pruned of outgroups)pruned_500_trees.treTerapontid species' tooth shape (anterior perspective)TPS shape files for terapontid species' tooth shape (anterior perspective)Anterior1.TPSTerapontid species' tooth shape (lateral perspective)TPS shape files for terapontid species' tooth shape (lateral perspective)Lateral-LM.TPS
DOI: 10.5061/dryad.684
title: Data from: Phylogeny of Saxifragales (angiosperms, eudicots): analysis of a rapid, ancient radiation

description: Rapid, ancient radiations pose one of the most difficult challenges for
 phylogenetic estimation. We employed DNA sequence data comprising 9,006
 aligned bp from five genes (chloroplast atpB, matK, rbcL, and 18S and 26S
 nrDNA) to elucidate relationships among major lineages of Saxifragales
 (angiosperms, eudicots). These relationships were poorly supported in
 prior studies, apparently because these lineages originated in rapid
 succession. Using an array of methods that explicitly incorporate
 assumptions about evolutionary process (weighted maximum parsimony,
 maximum likelihood, LogDet/paralinear transformed distances), we show that
 the initial diversification of Saxifragales was indeed rapid. We suggest
 that the poor resolution of our best phylogenetic estimate is not due to
 violations of assumptions or the combination of data partitions with
 conflicting histories or processes. We show that estimated branch lengths
 during the initial diversification are exceedingly short and we estimate
 that acquiring sufficient sequence data to resolve these relationships
 will require an extraordinary effort (~107 bp), assuming a linear increase
 in branch support with branch length. However, our simulation of much
 larger data sets containing a similar distribution of phylogenetic signal
 as the five sampled gene sequences suggests a limit to achievable branch
 support. We use statistical tests of differences in the likelihoods of
 topologies to evaluate whether the initial radiation of Saxifragales
 involved the simultaneous origin of major lineages. Our results are
 consist with predictions that resolving branching order of rapid, ancient
 radiations requires sampling characters that evolved rapidly at the time
 of the radiation, but have subsequently experienced a slower evolutionary
 rate.
description: 26S Data
 Set26S.nexus26S Revised Data Set26S.revised.nexusFishbein et al Data SetFishbein.nexusmatK Data SetmatK.nexus