cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8962
title: Data from: Reversal to air-driven sound production revealed by a molecular phylogeny of tongueless frogs, family Pipidae

description: BACKGROUND: Evolutionary novelties often appear by conferring completely
 new functions to pre- existing structures or by innovating the mechanism
 through which a particular function is performed. Sound production plays a
 central role in the behavior of frogs, which use their calls to delimit
 territories and attract mates. Therefore, frogs have evolved complex vocal
 structures capable of producing a wide variety of advertising sounds. It
 is generally acknowledged that most frogs call by moving an air column
 from the lungs through the glottis with the remarkable exception of the
 family Pipidae, whose members share a highly specialized sound production
 mechanism independent of air movement. RESULTS: Here, we performed
 behavioral observations in the poorly known African pipid genus
 Pseudhymenochirus and demonstrate that sound production in this aquatic
 frog is air-driven. However, morphological comparisons revealed an
 indisputable pipid nature of Pseudhymenochirus larynx. To place this
 paradoxical pattern into an evolutionary framework, we reconstructed
 robust molecular phylogenies of pipids based on complete mitochondrial
 genomes and nine nuclear protein-coding genes that coincided in placing
 Pseudhymenochirus nested among other pipids. CONCLUSIONS: We conclude that
 although Pseudhymenochirus has evolved a reversal to the ancestral
 non-pipid condition of air-driven sound production, the mechanism through
 which it occurs is an evolutionary innovation based on the derived larynx
 of pipids. This strengthens the idea that evolutionary solutions to
 functional problems often emerge based on previous structures, and for
 this reason, innovations largely depend on possibilities and constraints
 predefined by the particular history of each lineage.
description: Irisarri2011_Pipidae_nuclearNexus file containing the alignment of partial sequences of nine nuclear genes for anurans. The sequences correspond to data retrieved from GenBank and complemented with newly generated sequences of partial nuclear genes. In some cases, chimerical sequences were constructed by merging sequences from different species of the same genera, for which strong evidence exist of being monophyletic.Irisarri2011_Pipidae_mtgenomesNexus file containing the alignment of anuran mitochondrial genes. The sequences correspond to anuran taxa retrieved from GenBank plus the newly generated five mitochondrial genomes of pipoids.
DOI: 10.5061/dryad.s597d
title: Data from: Apparent vector-mediated parent-to-offspring transmission in an avian malaria-like parasite

description: Parasite transmission strategies strongly impact host–parasite
 co-evolution and virulence. However, studies of vector-borne parasites
 such as avian malaria have neglected the potential effects of host
 relatedness on the exchange of parasites. To test whether extended
 parental care in the presence of vectors increases the probability of
 transmission from parents to offspring, we used high-throughput sequencing
 to develop microsatellites for malaria-like Leucocytozoon parasites of a
 wild raptor population. We show that host siblings carry genetically more
 similar parasites than unrelated chicks both within and across years.
 Moreover, chicks of mothers of the same plumage morph carried more similar
 parasites than nestlings whose mothers were of different morphs,
 consistent with matrilineal transmission of morph-specific parasite
 strains. Ours is the first evidence of an association between host
 relatedness and parasite genetic similarity, consistent with
 vector-mediated parent-to-offspring transmission. The conditions for such
 ‘quasi-vertical’ transmission may be common and could suppress the
 evolution of pathogen virulence.
description: R code used in Chakarov
 et al. Apparent vector-mediated parent-to-offspring transmission in an
 avian malaria-like parasiteR code used in Chakarov
 et al. Apparent vector-mediated parent-to-offspring transmission in an
 avian malaria-like parasite, adaptation of source folder needed on
 setwd("C:/Users/Downloads")code_Chakarovetal_Apparent_mother_to offspring_transmission_of_Leucocytozoon.RGenotypes used by Chakarov et al. Apparent mother to offspring transmissiongenotypes from loci genotyped in 126 individuals for 15 loci described in Suppl. table 1 of Chakarov et al. "Apparent vector-mediated parent-to-offspring transmission in an avian malaria-like parasite"Dataset of Chakarov et al. vector-mediated parent-to-offspring transmissionDataset on genetic distance between Leucocytozoon infections of buzzard chicks with explanatory variables - similarity of chick morphs, mother's and father's morphs (0-different, 1- same), coordinates of both hosts, geographic distance between both hosts, time difference between both hosts, identity of host broods and host mothers.Lbuteonis coxIII as entered in Genbank KP640617Sequence of coxIII of Leucocytozoon buteonis from common buzzards from Eastern Westphalia, GermanyNestling table used by Chakarov et al apparent vector mediated parent to offspring transmissionPhenotypic data of nestlings used in Chakarov et al. including morphs of nestlings and parent, relative year of sampling and nest coordinatesLeucocytozoon buteonis microsatellites with flanking sequencesLeucocytozoon buteonis microsatellites with flanking sequences developed by Chakarov et al.
DOI: 10.5061/dryad.cf165
title: Data from: The influence of contemporary and historic landscape features on the genetic structure of the sand dune endemic, Cirsium pitcheri (Asteraceae)

description: Narrow endemics are at risk from climate change due to their restricted
 habitat preferences, lower colonization ability and dispersal distances.
 Landscape genetics combines new tools and analyses that allow us to test
 how both past and present landscape features have facilitated or hindered
 previous range expansion and local migration patterns, and thereby
 identifying potential limitations to future range shifts. We have compared
 current and historic habitat corridors in Cirsium pitcheri, an endemic of
 the linear dune ecosystem of the Great Lakes, to determine the relative
 contributions of contemporary migration and post-glacial range expansion
 on genetic structure. We used seven microsatellite loci to characterize
 the genetic structure for 24 populations of Cirsium pitcheri, spanning the
 center to periphery of the range. We tested genetic distance against
 different measures of geographic distance and landscape permeability,
 based on contemporary and historic landscape features. We found moderate
 genetic structure (ave Fst =0.14), and a north -south pattern to the
 distribution of genetic diversity and inbreeding, with northern
 populations having the highest diversity and lowest levels of inbreeding.
 High allelic diversity, small average pairwise distances and mixed genetic
 clusters identified in Structure suggest populations in the center of the
 range represent the point of entry to the Lake Michigan and a refugia of
 diversity for this species. A strong association between genetic distances
 and lake level changes suggests that historic lake fluctuations best
 explain the broad geographic patterns, and sandy habitat best explain
 local patterns or movement.
description: Microsatellite data and
 calculated Pairwise distanceRaw microsatellite data
 and the distances calculated in SPAGEDI and
 CircuitScapeRaw data for
 Dryad.xls
DOI: 10.5061/dryad.9fv56
title: Data from: Genetic structure and post-glacial expansion of Cornus florida L. (Cornaceae): integrative evidence from phylogeography, population demographic history, and species distribution modeling

description: Repeated global climatic cooling and warming cycles during the Pleistocene
 played a major role in the distribution and evolution of the Earth biota.
 Here, we integrate phylogeography, coalescent-based Bayesian estimation of
 demographic history, and species distribution modeling (SDM) to understand
 the genetic patterns and biogeography of the flowering dogwood, Cornus
 florida subsp. florida L., since the Last Glacial Maximum (LGM). Natural
 populations of the species are severely threatened by dogwood anthracnose.
 We genotyped 306 plants from 73 locations of the species across most of
 its native distribution with three DNA regions from the plastid genome,
 ndhF-rpl32, rps16 and trnQ-rps16. The genealogy and haplotype network
 reconstruction revealed two haplotype lineages diverging ∼3.70 million
 years ago. We detected no clear geographic structuring of genetic
 variation, although significant local structure appeared to be evident,
 likely due to a combination of substantial localized seed dispersal by
 small mammals and small population size/limited sampling at a location.
 The spatial distribution of haplotype frequencies, estimated population
 demographic history, and results from hindcasting analysis using SDM
 suggested refugia in southeastern North America and population reduction
 during the LGM, followed by rapid post-glacial expansion to the north.
 Forecasting analysis using SDM predicted range shifts to the north under
 ongoing global warming. Our results further suggested that gene flow via
 seed dispersal has been high but insufficient to counter the effect of
 genetic drift. This study demonstrates the benefit of integrating genetic
 data and species distribution modeling to obtain corroborative evidence in
 elucidating recent biogeographic history and understanding of genetic
 patterns and species evolution.
description: populationPooled sequence data with population information.Data pointOriginal data pointhaplotypeHaplotype file
DOI: 10.5061/dryad.m89k18s
title: Data from: Do parasites and antioxidant availability affect begging behaviour, growth rate and resistance to oxidative stress?

description: Early-life trade-offs faced by developing offspring can have long-term
 consequences for their future fitness. Young offspring use begging
 displays to solicit resources from their parents and have been selected to
 grow fast to maximize survival. However, growth and begging behaviour are
 generally traded-off against self-maintenance. Oxidative stress, a
 physiological mediator of life-history trade-offs, may play a major role
 in this trade-off by constraining, or being costly to, growth and begging
 behaviour. Yet, despite implications for the evolution of life-history
 strategies and parent-offspring conflicts, the interplay between growth,
 begging behaviour and resistance to oxidative stress remains to be
 investigated. We experimentally challenged wild great tit (Parus major)
 offspring by infesting nests with a common ectoparasite, the hen flea
 (Ceratophyllus gallinae), and simultaneously tested for compensating
 effects of increased vitamin E availability, a common dietary antioxidant.
 We further quantified the experimental treatment effects on offspring
 growth, begging intensity and oxidative stress. Flea-infested nestlings of
 both sexes showed reduced body mass during the first half of the nestling
 phase but this effect vanished short before fledging. Begging intensity
 and oxidative stress of both sexes were unaffected by both experimental
 treatments. Feeding rates were not affected by the experimental treatments
 but parents of flea-infested nests fed nestlings with a higher proportion
 of caterpillars, the main source of antioxidants. Additionally, female
 nestlings begged significantly less than males in control nests, while
 both sexes begged at similar rates in vitamin E supplemented nests. Our
 study shows that a parasite exposure does not necessarily affect oxidative
 stress levels or begging intensity, but suggests that parents can
 compensate for negative effects of parasitism by modifying food
 composition. Furthermore, our results indicate that the begging capacity
 of the less competitive sex is constrained by antioxidant availability.
description: Maronde_begging
 intensity and feeding rateMaronde_body_mass_repeatedMaronde_caterpillar_sizeMaronde_oxidative stress & fledging probabilityMaronde_proportion_caterpillar
DOI: 10.5061/dryad.m8jj7
title: Data from: Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm

description: Despite extensive studies on cultivated rice, the genetic structure and
 subdivision of this crop remain unclear at both global and local scales.
 Using 84 nuclear simple sequence repeat markers, we genotyped a panel of
 153 global rice cultivars covering all previously recognized groups and
 826 cultivars representing the diversity of Chinese rice germplasm. On the
 basis of model-based grouping, neighbour-joining tree and principal
 coordinate analysis, we confirmed the widely accepted five major groups of
 rice cultivars (indica, aus, aromatic, temperate japonica and tropical
 japonica), and demonstrated that rayada rice was unique in genealogy and
 should be treated as a new (the sixth) major group of rice germplasm. With
 reference to the global classification of rice cultivars, we identified
 three major groups (indica, temperate japonica and tropical japonica) in
 Chinese rice germplasm and showed that Chinese temperate japonica
 contained higher diversity than that of global samples, whereas Chinese
 indica and tropical japonica maintained slightly lower diversity than that
 present in the global samples. Particularly, we observed that all
 seasonal, drought-tolerant and endosperm types occurred within each of
 three major groups of Chinese cultivars, which does not support previous
 claims that seasonal differentiation exists in Indica and drought-tolerant
 differentiation is present in Japonica. It is most likely that
 differentiation of cultivar types arose multiple times stemming from
 artificial selection for adaptation to local environments.
description: Genetic Diversity and
 Classification of Oryza sativa with Emphasis on Chinese Rice
 GermplasmOriginal
 data.xlsx
DOI: 10.5061/dryad.b708j
title: Data from: The impact of shifts in marine biodiversity hotspots on patterns of range evolution: evidence from the Holocentridae (squirrelfishes and soldierfishes)

description: One of the most striking biodiversity patterns is the uneven distribution
 of marine species richness, with species diversity in the Indo-Australian
 Archipelago (IAA) exceeding all other areas. However, the IAA formed
 fairly recently, and marine biodiversity hotspots have shifted across
 nearly half the globe since the Paleogene. Understanding how lineages have
 responded to shifting biodiversity hotspots represents a necessary
 historic perspective on the formation and maintenance of global marine
 biodiversity. Such evolutionary inferences are often challenged by a lack
 of fossil evidence that provide insights into historic patterns of
 abundance and diversity. The greatest diversity of squirrelfishes and
 soldierfishes (Holocentridae) is in the IAA, yet these fishes also
 represent some of the most numerous fossil taxa in deposits of the former
 West Tethyan biodiversity hotspot. We reconstruct the pattern of
 holocentrid range evolution using time-calibrated phylogenies that include
 most living species and several fossil lineages, demonstrating the
 importance of including fossil species as terminal taxa in ancestral area
 reconstructions. Holocentrids exhibit increased range fragmentation
 following the West Tethyan hotspot collapse. However, rather than
 originating within the emerging IAA hotspot, the IAA has acted as a
 reservoir for holocentrid diversity that originated in adjacent regions
 over deep evolutionary time scales.
description: Dornburgetal_All_genesANDMorphnexus data file3TIMESLICEconstrainedlagrange input file8TIMESLICEconstrainedlagrange input fileWith_fossils_range_Holocentridaerange dataWithNO_fossils_range_Holocentridaerange dataresampled_nofossils.conchronogram with no fossilsresampled_withfossils.conchronogram with fossils
DOI: 10.5061/dryad.50s5g5q
title: Data from: Integrated evidence reveals a new species in the ancient blue coral genus Heliopora (Octocorallia)

description: Maintaining the accretion potential and three dimensional structure of
 coral reefs is a priority but reef-building scleractinian corals are
 highly threatened and retreating. Hence future reefs are predicted to be
 dominated by non-constructional taxa. Since the Late Triassic however,
 other non-scleractinian anthozoans such as Heliopora have contributed to
 tropical and subtropical reef-building. Heliopora is an ancient and highly
 conserved reef building octocoral genus within the monospecific Family
 Helioporidae, represented by a single extant species – H. coerulea,
 Pallas, 1766. Here we show integrated morphological, genomic and
 reproductive evidence to substantiate the existence of a second species
 within the genus Heliopora. Importantly, some individuals of the new
 species herein described as Heliopora hiberniana sp. nov. feature a white
 skeleton indicating that the most diagnostic and conserved Heliopora
 character (the blue skeleton) can be displaced. The new species is
 currently known only from offshore areas in north Western Australia, which
 is a part of the world where coral bleaching events have severely impacted
 the scleractinian community over the last two decades. Field observations
 indicate individuals of both H. coerulea and H. hiberniana sp. nov. were
 intact after the 2016 Scott Reef thermal stress event, and we discuss the
 possibility that bleaching resistant non-scleractinian reef builders such
 as Heliopora could provide new ecological opportunities for the
 reconfiguration of future reefs by filling empty niches and functional
 roles left open by the regression of scleractinian corals.
description: SNPsData170804_Heliopora_0.7This includes 3 different SNPs Dataset in each Tab (MIG-seq Original Data(166), Mapped (146), Unmapped(20)) includes SNPs obtained from MIG-seq analysis.WesternAustraliaSSRdataSubmittedMicrosatellite data used in Zoe et al (2018)Warning: Although the consistency of genotyping was confirmed within this dataset, we strongly recommend not to merge with other microsatellite dataset genotyped by different methods or machine.
DOI: 10.5061/dryad.1362
title: Data from: Historical divergence versus contemporary gene flow: evolutionary history of the calcicole Ranunculus alpestris group (Ranunculaceae) in the European Alps and the Carpathians

description: Although many species have similar total distributional ranges, they might
 be restricted to very different habitats and might have different
 phylogeographic histories. In the European Alps, our excellent knowledge
 of the evolutionary history of silicate-dwelling plants is contrasted by a
 virtual lack of data from limestone-dwelling plants. These two categories
 are expected to differ strongly with respect to their glacial history. The
 calcicole Ranunculus alpestris group comprises three diploid species of
 alpine habitats. Analyses of AFLP fingerprints and matK sequences gave
 incongruent results, indicative for reticulate evolution. Our data
 highlight historical episodes of range fragmentation and expansion,
 occasional long distance dispersal and on-going gene flow as important
 processes shaping the genetic structure of the group. Genetic divergence
 seems a better indicator of historical processes than patterns of genetic
 diversity, which rather mirror contemporary processes as connectivity of
 populations and population sizes. Three phylogeographical subgroups have
 been found within the R. alpestris group, neither following taxonomy nor
 geography. Genetic heterogeneity in the Southern Alps contrasts with
 Northern Alpine uniformity. The Carpathians have been stepwise colonised
 from the Eastern Alpine lineage resulting in a marked diversity loss in
 the Southern Carpathians. The main divergence within the group, separating
 the ancestor of the two endemic species from R. alpestris s. str.,
 predates the Quaternary. Therefore, range shifts produced by paleoclimatic
 oscillations seem to have acted on the genetic structure of R. alpestris
 group on a more regional level, e.g. triggering an allopatric separation
 of R. traunfellneri from R. bilobus.
description: AFLP data for Ranunculus
 alpestris groupRal_database.xls
DOI: 10.5061/dryad.9b56t
title: Data from: The active participation of German-speaking countries in conferences of the Association for Medical Education in Europe (AMEE) between 2005 and 2013: a reflection of the development of medical education research?

description: Objectives: Medical education is gaining in significance internationally.
 A growing interest in the field has been observed in German-speaking
 countries (Austria, Germany, Switzerland) since the early 2000s. This
 interest is not, however, reflected in an increase in the number of
 publications on medical education of German-speaking authors in
 international professional journals. The following investigation examines
 the potential use of active participant numbers of German-speaking
 researchers at AMEE conferences as a means of measuring said development.
 Methods: The AMEE conference proceedings from the categories poster
 presentations, short communications, research papers and plenary
 presentations from the years 2005-2013 were examined for evidence of
 Austrian, German and Swiss participation. The abstracts were subsequently
 analysed in terms of content and categorised according to study design,
 methodology, object of study, and research topic. Results: Of the 9,446
 analysed abstracts, 549 contributions show at least one first, last or
 co-author from Austria, Germany or Switzerland. The absolute number of
 contributions per conference varied between 44 in 2010 and 77 in 2013. The
 percentage fluctuated between 10% in 2005 and 4.1% in 2010. From the year
 2010 onwards, however, participation increased continually. The research
 was predominantly descriptive (62.7%). Studies on fundamental questions of
 teaching and learning (clarification studies) were less frequent (4.0%).
 For the most part, quantitative methods (51.9%) were implemented in
 addressing subjects such as learning and teaching methods (33%),
 evaluation and assessment (22.4%) or curriculum development (14.4%). The
 study population was usually comprised of students (52.5%). Conclusions:
 The number of contributions from Austria, Germany and Switzerland peak at
 the beginning and at the end of the evaluated period of time. A continual
 increase in active participation since 2005 was not observed. These
 observations do not reflect the actual increase of interest in medical
 education research in German-speaking countries.
description: German-speaking AMEE
 participation 2005-2013AMEE 2005-2013 Beiträge mit
 dt. Beteiligung-neu.sav