cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mj74q
title: Data from: Identification of source-sink dynamics in mountain lions of the Great Basin

description: Natural and anthropogenic boundaries have been shown to affect population
 dynamics and population structure for many species with movement patterns
 at the landscape level. Understanding population boundaries and movement
 rates in the field for species that are cryptic and occur at low densities
 is often extremely difficult and logistically prohibitive; however genetic
 techniques may offer insights that have previously been unattainable. We
 analyzed thirteen microsatellite loci for 739 mountain lions (Puma
 concolor) using muscle tissue samples from individuals in the Great Basin
 throughout Nevada and the eastern Sierra Nevada mountain range to test the
 hypothesis that heterogeneous hunting pressure results in source-sink
 dynamics at the landscape scale. We used a combination of non-spatial and
 spatial model-based Bayesian clustering methods to identify genetic
 populations. We then used a recently developed Bayesian multilocus
 genotyping method to estimate asymmetrical rates of contemporary movement
 between those sub-populations and to identify source and sink populations.
 We identified 2 populations at the highest level of genetic structuring
 with a total of 5 subpopulations in the Great Basin of Nevada and the
 eastern Sierra Nevada range. Our results suggest that source-sink dynamics
 occur at landscape scales for wide-ranging species, such as mountain
 lions, and that source populations may be those that are under relatively
 less hunting pressure and that occupy refugia.
description: Accessible Data
 SpreadsheetMicrosatellite genotype
 data and sampling locations used for analyses for 739
 Pumas.
DOI: 10.5061/dryad.120f8
title: Data from: Rivers, refuges, and population divergence of fire-eye antbirds (Pyriglena) in the Amazon Basin

description: The identification of ecological and evolutionary mechanisms that might
 account for the elevated biotic diversity in tropical forests is a central
 theme in evolutionary biology. This issue is especially relevant in the
 Neotropical region, where biological diversity is the highest in the
 world, but where few studies have been conducted to test factors causing
 population differentiation and speciation. We used mtDNA sequence data to
 examine the genetic structure within white-backed fire-eye (Pyriglena
 leuconota) populations along the Tocantins River valley in the
 south-eastern Amazon Basin, and we confront the predictions of the river
 and the Pleistocene refuge hypotheses with patterns of genetic variation
 observed in these populations. We also investigated whether these patterns
 reflect the recently detected shift in the course of the Tocantins River.
 We sampled a total of 32 individuals east of, and 52 individuals west of,
 the Tocantins River. Coalescent simulations and phylogeographical and
 population genetics analytical approaches revealed that mtDNA variation
 observed for fire-eye populations provides little support for the
 hypothesis that populations were isolated in glacial forest refuges.
 Instead, our data strongly support a key prediction of the river
 hypothesis. Our study shows that the Tocantins River has probably been the
 historical barrier promoting population divergence in fire-eye antbirds.
 Our results have important implications for a better understanding of the
 importance of large Amazonian rivers in vertebrate diversification in the
 Neotropics.
description: Pyriglena
 leuconotanexus file with
 sequences of mtDNA ND2Pyriglenaleuconota.nxsPyriglenaleuconotaSEQUENCESExcel file with information about sequences in the file "Pyriglenaleuconota"Pyriglenaleuconotaallsequennexus file with all mtDNA ND2 sequences. Please contact the first author for any further details.
DOI: 10.5061/dryad.vk67d
title: Data from: Polymorphism pattern at a Miniature Inverted-repeat Transposable Element locus downstream of the domestication gene Teosinte-branched1 in wild and domesticated pearl millet

description: Unraveling the mechanisms involved in adaptation to understand plant
 morphological evolution is a challenging goal. For crop species,
 identification of molecular causal polymorphisms involved in domestication
 traits are central to this issue. Pearl millet, a domesticated grass
 mostly found in semi-arid areas of Africa and India, is an interesting
 model to address this topic: the domesticated form shares common derived
 phenotypes with some other cereals such as a decreased ability to develop
 basal and axillary branches in comparison with the wild phenotype. Two
 recent studies have shown that the orthologue of the maize gene
 Teosinte-Branched1 in pearl millet (PgTb1) was likely involved in
 branching evolution during domestication and that a Miniature
 Inverted-repeat Transposable Element (MITE) of the Tuareg family was
 inserted in the 3'-untranslated region of PgTb1. For a set of 35 wild
 and domesticated populations, we compared the polymorphism patterns at
 this MITE and at microsatellite loci. The Tuareg insertion was nearly
 absent in the wild populations, whereas a strong longitudinal frequency
 cline was observed in the domesticated populations. The geographic pattern
 revealed by neutral microsatellite loci clearly demonstrated that
 isolation by distance does not account for the existence of this cline.
 However, comparison of population differentiation at the microsatellite
 and the MITE loci and analyses of the nucleotide polymorphism pattern in
 the downstream region of PgTb1 did not show evidence that the cline at the
 MITE locus has been shaped by selection, suggesting the implication of a
 neutral process. Alternative hypotheses are discussed.
description: Microsatellite_and_MITE_data
DOI: 10.5061/dryad.sp58m
title: Data from: Modelling the two-locus architecture of divergent pollinator adaptation: how variation in SAD paralogues affects fitness and evolutionary divergence in sexually deceptive orchids

description: Divergent selection by pollinators can bring about strong reproductive
 isolation via changes at few genes of large effect. This has recently been
 demonstrated in sexually deceptive orchids, where studies (1) quantified
 the strength of reproductive isolation in the field; (2) identified genes
 that appear to be causal for reproductive isolation; and (3) demonstrated
 selection by analysis of natural variation in gene sequence and
 expression. In a group of closely related Ophrys orchids, specific floral
 scent components, namely n-alkenes, are the key floral traits that control
 specific pollinator attraction by chemical mimicry of insect sex
 pheromones. The genetic basis of species-specific differences in alkene
 production mainly lies in two biosynthetic genes encoding stearoyl–acyl
 carrier protein desaturases (SAD) that are associated with floral scent
 variation and reproductive isolation between closely related species, and
 evolve under pollinator-mediated selection. However, the implications of
 this genetic architecture of key floral traits on the evolutionary
 processes of pollinator adaptation and speciation in this plant group
 remain unclear. Here, we expand on these recent findings to model
 scenarios of adaptive evolutionary change at SAD2 and SAD5, their effects
 on plant fitness (i.e., offspring number), and the dynamics of speciation.
 Our model suggests that the two-locus architecture of reproductive
 isolation allows for rapid sympatric speciation by pollinator shift;
 however, the likelihood of such pollinator-mediated speciation is
 asymmetric between the two orchid species O. sphegodes and O. exaltata due
 to different fitness effects of their predominant SAD2 and SAD5 alleles.
 Our study not only provides insight into pollinator adaptation and
 speciation mechanisms of sexually deceptive orchids but also demonstrates
 the power of applying a modeling approach to the study of
 pollinator-driven ecological speciation.
description: FieldworkExtractThe GC data from Ophrys samples. SD refers to 300ng internal standard (C18 alkane). Population and species information were indicated in the Xu. at al. 2011 Evolution and Xu. et.al 2012 PloS Genet.Pollinator_attraction_allPredicted Pollinator attraction. This data is presented as barplot as Figure 3.Alkene_composition_allPredicted alkene compositions of different hypothetic genotypes. This figure was plotted as Figure 2.SAD_Two_locus_model_05.4This is the R code used to produce the model presented in this manuscript. I have annotated the functions for major steps. However, if any questions related to this R script, please contact me: sxu@ice.mpg.deTwo_locus_model_05.4.R
DOI: 10.5061/dryad.5dk2fs5
title: Data from: X-chromosome meiotic drive in Drosophila simulans: a QTL approach reveals the complex polygenic determinism of Paris drive suppression

description: Meiotic drivers are selfish genetic elements that promote their own
 transmission into the gametes, which results in intragenomic conflicts. In
 the Paris sex-ratio system of Drosophila simulans, drivers located on the
 X chromosome prevent the segregation of the heterochromatic Y chromosome
 during meiosis II, and hence the production of Y-bearing sperm. The
 resulting sex-ratio bias strongly impacts population dynamics and
 evolution. Natural selection, which tends to restore an equal sex ratio,
 favors the emergence of resistant Y chromosomes and autosomal suppressors.
 This is the case in the Paris sex-ratio system where the drivers became
 cryptic in most of the natural populations of D. simulans. Here, we used a
 Quantitative Trait Locus (QTL) mapping approach based on the analysis of
 152 highly recombinant inbred lines (RILs) to investigate the genetic
 determinism of autosomal suppression. The RILs were derived from an
 advanced intercross between two parental lines, one showing complete
 autosomal suppression while the other one was sensitive to drive. The
 confrontation of RIL autosomes with a reference XSR chromosome allowed us
 to identify two QTLs on chromosome 2 and three on chromosome 3, with
 strong epistatic interactions. Our findings highlight the multiplicity of
 actors involved in this intragenomic battle over the sex ratio.
description: data_RILgenotypeThis data file contains all the RILs genotypes and the genetic position for each markers.data.csv
DOI: 10.5061/dryad.8q931
title: Data from: The location of the citation: changing practices in how publications cite original data in the Dryad Digital Repository

description: While stakeholders in scholarly communication generally agree on the
 importance of data citation, there is not consensus on where those
 citations should be placed within the publication – particularly when the
 publication is citing original data. Recently, CrossRef and the Digital
 Curation Center (DCC) have recommended as a best practice that original
 data citations appear in the works cited sections of the article. In some
 fields, such as the life sciences, this contrasts with the common practice
 of only listing data identifier(s) within the article body
 (intratextually). We inquired whether data citation practice has been
 changing in light of the guidance from CrossRef and the DCC. We examined
 data citation practices from 2011 to 2014 in a corpus of 1,125 articles
 associated with original data in the Dryad Digital Repository. The
 percentage of articles that include no reference to the original data has
 declined each year, from 31% in 2011 to 15% in 2014. The percentage of
 articles that include data identifiers intratextually has grown from 69%
 to 83%, while the percentage that cite data in the works cited section has
 grown from 5% to 8%. If the proportions continue to grow at the current
 rate of 19-20% annually, the proportion of articles with data citations in
 the works cited section will not exceed 90% until 2030.
description: Citation location
 resultsDetails of the articles
 analyzed to determine the location of original data identifiers within the
 article. Only includes results for articles that were Open Access and
 full-text indexed in EPMC.citation_locations.txtCitation location scriptThis Python script imports lists of Dryad metadata and uses it to search Europe PMC and to locate and classify data references appearing in the literature.citation_locations.py
DOI: 10.5061/dryad.7vb83
title: Data from: Barb geometry of asymmetrical feathers reveals a transitional morphology in the evolution of avian flight

description: The geometry of feather barbs (barb length and barb angle) determines
 feather vane asymmetry and vane rigidity, which are both critical to a
 feather's aerodynamic performance. Here, we describe the relationship
 between barb geometry and aerodynamic function across the evolutionary
 history of asymmetrical flight feathers, from Mesozoic taxa outside of
 modern avian diversity (Microraptor, Archaeopteryx, Sapeornis,
 Confuciusornis and the enantiornithine Eopengornis) to an extensive sample
 of modern birds. Contrary to previous assumptions, we find that barb angle
 is not related to vane-width asymmetry; instead barb angle varies with
 vane function, whereas barb length variation determines vane asymmetry. We
 demonstrate that barb geometry significantly differs among functionally
 distinct portions of flight feather vanes, and that cutting-edge leading
 vanes occupy a distinct region of morphospace characterized by small barb
 angles. This cutting-edge vane morphology is ubiquitous across a
 phylogenetically and functionally diverse sample of modern birds and
 Mesozoic stem birds, revealing a fundamental aerodynamic adaptation that
 has persisted from the Late Jurassic. However, in Mesozoic taxa stemward
 of Ornithurae and Enantiornithes, trailing vane barb geometry is
 distinctly different from that of modern birds. In both modern birds and
 enantiornithines, trailing vanes have larger barb angles than in
 comparatively stemward taxa like Archaeopteryx, which exhibit small
 trailing vane barb angles. This discovery reveals a previously
 unrecognized evolutionary transition in flight feather morphology, which
 has important implications for the flight capacity of early feathered
 theropods such as Archaeopteryx and Microraptor. Our findings suggest that
 the fully modern avian flight feather, and possibly a modern capacity for
 powered flight, evolved crownward of Confuciusornis, long after the origin
 of asymmetrical flight feathers, and much later than previously
 recognized.
description: Feo-2015_PRSB_PaperDataMeasurements of modern flying, modern flightless, and Mesozoic stem bird feathers.
DOI: 10.5061/dryad.2np32
title: Data from: Gut microbiota modifies olfactory-guided microbial preferences and foraging decisions in Drosophila

description: The gut microbiota affects a wide spectrum of host physiological traits,
 including development [ 1–5 ], germline [ 6 ], immunity [ 7–9 ], nutrition
 [ 4, 10, 11 ], and longevity [ 12, 13 ]. Association with microbes also
 influences fitness-related behaviors such as mating [ 14 ] and social
 interactions [ 15, 16 ]. Although the gut microbiota is evidently
 important for host wellbeing, how hosts become associated with particular
 assemblages of microbes from the environment remains unclear. Here, we
 present evidence that the gut microbiota can modify microbial and
 nutritional preferences of Drosophila melanogaster. By experimentally
 manipulating the gut microbiota of flies subjected to behavioral and
 chemosensory assays, we found that fly-microbe attractions are shaped by
 the identity of the host microbiota. Conventional flies exhibit preference
 for their associated Lactobacillus, a behavior also present in axenic
 flies as adults and marginally as larvae. By contrast, fly preference for
 Acetobacter is primed by early-life exposure and can override the innate
 preference. These microbial preferences are largely olfactory guided and
 have profound impact on host foraging, as flies continuously trade off
 between acquiring beneficial microbes and balancing nutrients from food.
 Our study shows a role of animal microbiota in shaping host
 fitness-related behavior through their chemosensory responses, opening a
 research theme on the interrelationships between the microbiota, host
 sensory perception, and behavior.
description: Data from: Gut
 microbiota modifies olfactory-guided microbial preferences and foraging
 decisions in DrosophilaThe file contains the
 raw data set for the Manuscript with the title mentioned above. Files are
 separated by figures, each in its individual tab within the Excel file.
 Variable names are self-explanatory.Wong et al
 2017-RawData-perfigure.xlsx
DOI: 10.5061/dryad.17hf071
title: Data from: Tracking dragons: stable isotopes reveal the annual cycle of a long-distance migratory insect

description: Insect migration is globally ubiquitous and can involve continental-scale
 movements and complex life-histories. Apart from select species of
 migratory moths and butterflies, little is known about the structure of
 the annual cycle for migratory insects. Using stable-hydrogen isotope
 analysis of 852 wing samples from eight countries spanning 140 years,
 combined with 21 years of citizen science data, we determined the full
 annual cycle of a large migratory dragonfly, the common green darner (Anax
 junius). We demonstrate that darners undertake complex long-distance
 annual migrations governed largely by temperature that involve at least
 three generations. In spring, the first generation makes a long-distance
 northbound movement (&gt;650 km) from southern to northern range
 limits, lays eggs and dies. A second generation emerges and returns south
 (&gt;680 km), where they lay eggs and die. Finally, a third resident
 generation emerges, reproducing locally and giving rise to the cohort that
 migrates north the following spring. Since migration timing and nymph
 development are highly dependent on temperature, continued climate change
 could lead to fundamental changes in the biology for this and similar
 migratory insects.
description: Observed Flight
 datesThis file contains the
 first flight date information for adult Common green darners (Anax junius)
 used to generate Fig 1.FlightTimes.csvGreen Darner Isotope dataThis file contains isotope data used to make natal geographic assignments to reveal the annual cycle and migration of the Common green darner (Anax junius).MDPsamples_PredictedDvalues.csvGBIF.orgData were acquired from GBIF.org and were used to generate a habitat suitability surface for the common green darner (Anax junius). Citation: GBIF.org (03 July 2018) GBIF Occurrence Download https://doi.org/10.15468/dl.pw0uol
DOI: 10.5061/dryad.j939d
title: Data from: Vanishing chromosomal inversion clines in Drosophila subobscura from Chile: is behavioral thermoregulation to blame?

description: Chromosomal inversion clines paralleling the long-standing ones in native
 Palearctic populations of Drosophila subobscura evolved swiftly after this
 species invaded the Americas in the late 1970s and early 1980s. However,
 the new clines did not consistently continue to converge on the Old World
 baseline. Our recent survey of Chilean populations of D. subobscura shows
 that inversion clines have faded or even changed sign with latitude. Here,
 we investigate the hypothesis that this fading of inversion clines might
 be due to the Bogert effect, namely, that flies’ thermoregulatory behavior
 has eventually compensated for environmental variation in temperature,
 thus buffering selection on thermal-related traits. We show that
 latitudinal divergence in thermal preference (Tp) has evolved in Chile for
 females, with higher-latitude flies having a lower mean Tp. Plastic
 responses in Tp also lessen latitudinal thermal variation because flies
 developed at colder temperatures prefer warmer microclimates. Our results
 are consistent with the idea that active behavioral thermoregulation might
 buffer environmental variation and reduce the potential effect of thermal
 selection on other traits as chromosomal arrangements.
description: Thermal preference of
 Drosophila subobscura sampled along a latitudinal gradient in
 ChileDsubobscura_TpChile2010.xls
DOI: 10.5061/dryad.41pn9
title: Data from: Rapid independent trait evolution despite a strong pleiotropic genetic correlation

description: Genetic correlations are the most commonly studied of all potential
 constraints on adaptive evolution. We present a comprehensive test of
 constraints caused by genetic correlation, comparing empirical results to
 predictions from theory. The additive genetic correlation between the
 filament and corolla tube in wild radish flowers is very high in
 magnitude, estimated with good precision (0.85 ± 0.06), and is caused by
 pleiotropy. Thus, evolutionary changes in the relative lengths of these
 two traits should be constrained. Still, artificial selection produced
 rapid evolution of these traits in opposite directions, so that the
 difference between them in one replicate increased by six standard
 deviations relative to controls in only nine generations. This would
 result in a 54% increase in relative fitness based on a previous estimate
 of natural selection in this population, and would produce the phenotypes
 found in the most extreme species in the family Brassicaceae in less than
 100 generations. These responses were within theoretical expectations and
 much slower than if the genetic correlation was zero; thus, there was
 evidence for constraint. These results, coupled with comparable results
 from other species, show that evolution can be rapid despite the
 constraints caused by genetic correlations.
description: Artificial selection on
 anther exsertion in wild radishConnerArtSelData.csv
DOI: 10.5061/dryad.r2j05j8
title: Data from: Natural and sexual selection on cuticular hydrocarbons: a quantitative genetic analysis

description: While the reproductive benefits of sexual displays have been widely
 studied, we have relatively limited evidence of the fitness costs
 associated with most display traits. Insect cuticular hydrocarbon (CHC)
 profiles are sexually selected traits that also protect against
 desiccation. These two functions are thought to oppose each other, with
 investment in particular compounds believed to increase attractiveness at
 the expense of compounds that protect against water-loss. We investigated
 this potential trade-off in a quantitative genetic framework using the
 Australian field cricket, Teleogryllus oceanicus. Several compounds were
 significantly genetically correlated with either attractiveness or
 desiccation resistance. Of these compounds, one was negatively genetically
 correlated with attractiveness but positively genetically correlated with
 desiccation resistance. Furthermore, scoring each individual’s overall CHC
 profile for its level of attractiveness and desiccation resistance
 indicated a negative genetic correlation between these multivariate
 phenotypes. Together, our results provide evidence for a genetic trade-off
 between sexually and naturally selected functions of the CHC profile. We
 suggest that the production of an attractive CHC profile may be costly for
 males, but highlight the need for further work to support this finding
 experimentally. Genetic covariation between the CHC profile and
 attractiveness suggests that females can gain attractive sons through
 female choice.
description: Data_for_Berson_et_al_2019_Proc_BFile containing the attractiveness, desiccation resistance and cuticular hydrocarbon (CHC) data.Pedigree_for_Berson_et_al_2019_Proc_BFile containing the pedigree data.READMEFile describing the data and pedigree.