cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3gq3gc6
title: Data from: The adaptive significance of chromosomal inversion polymorphisms in Drosophila melanogaster

description: Chromosomal inversions, structural mutations that reverse a segment of a
 chromosome, cause suppression of recombination in the heterozygous state.
 Several studies have shown that inversion polymorphisms can form clines or
 fluctuate predictably in frequency over seasonal time spans. These
 observations prompted the hypothesis that chromosomal rearrangements might
 be subject to spatially and/or temporally varying selection. Here we
 review what has been learned about the adaptive significance of inversion
 polymorphisms in the vinegar fly Drosophila melanogaster, the species in
 which they were first discovered by Sturtevant in 1917. A large body of
 work provides compelling evidence that several inversions in this system
 are adaptive; however, the precise selective mechanisms that maintain them
 polymorphic in natural populations remain poorly understood. Recent
 advances in population genomics, modeling and functional genetics promise
 to greatly improve our understanding of this longstanding and fundamental
 problem in the near future.
description: Worldwide Inversion
 frequencies of Drosophila melanogasterThis table, which is
 equivalent to Table S1 in the Supporting Information, contains meta
 information and frequencies of four common cosmopolitain inversions
 (In2L)t, In(2R)NS, In(3L)P and In(3R)Payne) that were assembled from 34
 independent datasets which span more than 50 years of
 collections.Table
 S1.xlsx
DOI: 10.5061/dryad.rj480
title: Data from: Relationships between resprouting ability, species traits, and resource allocation patterns in woody species in a temperate forest

description: Many woody plants resprout to restore above-ground biomass after
 disturbances or to survive in stressful environments. Resprouting requires
 carbohydrate storage, but the general relationship between resource
 allocation patterns and resprouting ability remains unclear because it can
 be influenced by the disturbance regime to which species have adapted. We
 studied deciduous broadleaved trees that coexist in a Japanese
 cool-temperate forest to investigate the relationships among the biomass
 and total non-structural carbohydrate (TNC) allocation patterns of
 saplings, resprouting ability and functional traits. The study species
 comprised 16 single-stemmed species that only resprout when above-ground
 biomass loss occurs and eight multi-stemmed species that resprout
 regardless of whether above-ground damage occurs or not. Single-stemmed
 species with better juvenile resprouting ability had larger roots, whereas
 multi-stemmed species with better juvenile resprouting ability did not
 necessarily depend on below-ground reserves. Species that retain their
 ability to resprout until a larger size had a higher root TNC content as
 saplings, suggesting that they can survive major disturbances such as fire
 and coppicing by resprouting supported by TNC stored in their roots.
 Species with shade-tolerant traits (i.e. low foliar nitrogen indicating
 low photosynthetic capacity, high wood density indicating high defensive
 investment) had small below-ground TNC reserves irrespective of
 resprouting types. On the other hand, multi-stemmed species with high wood
 density and high LMA (indicating high photosynthetic capacity) had small
 above-ground TNC reserves. Contrary to our hypothesis, a species’ maximum
 size did not relate to the size of its below-ground reserves. By
 considering the differences in resprouting types, we suggest more complex
 control of resprouting than was formerly proposed. Variation in the
 resprouting ability of single-stemmed species was based on a trade-off
 between below-ground reserves for resprouting and shade-tolerant traits.
 However, multi-stemmed species can vigorously resprout irrespective of the
 size of its below-ground reserves. Their multi-stemmed architecture,
 well-defended wood, high photosynthetic capacity or large above-ground
 carbohydrate reserves seem to respectively contribute to their
 persistence. Such variation in the resprouting strategy based on a
 trade-off between shade tolerance and resource storage would promote
 species coexistence under a range of disturbance regimes and light
 environments.
description: FEShibataDataForAnalyses
DOI: 10.5061/dryad.h8j57
title: Data from: Parasitic infection: a buffer against ocean acidification?

description: Recently, there has been a concerted research effort by marine scientists
 to quantify the sensitivity of marine organisms to ocean acidification
 (OA). Empirical data generated by this research have been used to predict
 changes to marine ecosystem health, biodiversity and productivity that
 will be caused by continued acidification. These studies have also found
 that the effects of OA on marine organisms can be significantly modified
 by additional abiotic stressors (e.g. temperature or oxygen) and biotic
 interactions (e.g. competition or predation). To date, however, the
 effects of parasitic infection on the sensitivity of marine organisms to
 OA have been largely ignored. We show that parasitic infection
 significantly altered the response of a marine gastropod to simulated OA
 conditions by reducing the mortality of infected individuals relative to
 uninfected conspecifics. Without the inclusion of infection data, our
 analysis would not have detected the significant effect of pH on host
 mortality. These results strongly suggest that parasitic infection may be
 an important confounding factor in OA research and must be taken into
 consideration when assessing the response of marine species to OA.
description: MacLeodPoulin_2016_BLSnail survival data
DOI: 10.5061/dryad.5p3mt
title: Data from: How efficient is Apis cerana (Hymenoptera: Apidae) in pollinating cabbage, Brassica oleracea var. capitata? pollination behavior, pollinator effectiveness, pollinator requirement, and impact of pollination

description: Cabbage is a cross-pollinated crop because of sporophytic
 self-incompatibility, and honey bees play an important role in its
 pollination. Though Asian honey bees, Apis cerana F., are used in
 pollination of cabbage, the rate of visitation, behavior, pollinator
 efficacy, and impact on seed-set are to be determined. Apis cerana occupy
 a share of 19.18% of all the flower visitors of cabbage in natural habitat
 of North Western Indian Himalayas. Pollination behavior in terms of peak
 activity, flowers processed per unit time, time spent per flower, and time
 spent in search of flowers are studied separately for both pollen and
 nectar foragers. Pollinator effectiveness as measured by seed set in
 flowers excluded from bee visitation, single bee visit, and unrestricted
 pollinator visits was 0.11. Studies on the impact of A. cerana bee
 pollination in cabbage seed production revealed an increase of 17.28% in
 siliqua per panicle, with 26.11% increase in seed yield. For assessing the
 requirement of A. cerana to pollinate one hectare of cabbage, flower
 availability and the speed with which the pollen and nectar foragers
 process the flowers are taken into consideration. A forager is estimated
 to pollinate 4,780 flowers a day, but cabbage flower requires 9.09 visits
 of A. cerana for optimum seed set. Thus, a maximum of 4,999 bee foragers
 or 8.33 colonies are needed to effectively pollinate 1 ha of cabbage.
 Though A. cerana is a good pollinator, our findings suggest that it is not
 an ideal pollinator of cabbage.
description: Tables
 cabbageData on pollinator
 density, pollination behavior and impact of pollination
DOI: 10.5061/dryad.g14qq07
title: Data from: Interacting effects of predation risk and resource level on escape speed of amphibian larvae along a latitudinal gradient

description: Fast-growing genotypes living in time-constrained environments are often
 more prone to predation, suggesting that growth-predation risk trade-offs
 are important factors maintaining variation in growth along climatic
 gradients. However, the mechanisms underlying how fast growth increases
 predation-mediated mortality are not well understood. Here, we
 investigated if slow-growing, low-latitude individuals have faster escape
 swimming speed than fast-growing high-latitude individuals using common
 frog (Rana temporaria) tadpoles from eight populations collected along a
 1500 km latitudinal gradient. We measured escape speed in terms of burst
 and endurance speeds in tadpoles raised in the laboratory at two food
 levels and in the presence and absence of a predator (Aeshna dragonfly
 larvae). We did not find any latitudinal trend in escape speed
 performance. In low food treatments, burst speed was higher in tadpoles
 reared with predators but did not differ between high food treatments.
 Endurance speed, on the contrary, was lower in high-food tadpoles reared
 with predators, and did not differ between treatments at low food levels.
 Tadpoles reared with predators showed inducible morphology (increased
 relative body size and tail depth), which had positive effects on speed
 endurance at low but not at high food levels. Burst speed was positively
 affected by tail length and tail muscle size in the absence of predators.
 Our results suggest that escape speed does not trade off with fast growth
 along the latitudinal gradient in R. temporaria tadpoles. Instead, escape
 speed is a plastic trait and strongly influenced by the interaction
 between resource level and predation risk.
description: Lindgrenetal2018_dataContainer-specific means of swimming speed variables, life-history traits and log-transformed morphology.Lindgrenetal2018.xls
DOI: 10.5061/dryad.8795
title: Data from: Altered gene expression and ecological divergence in sibling allopolyploids of Dactylorhiza (Orchidaceae)

description: Background: Hybridization and polyploidy are potent forces that have
 regularly stimulated plant evolution and adaptation. Dactylorhiza majalis
 s.s., D. traunsteineri s.l. and D. ebudensis are three allopolyploid
 species of a polyploid complex formed through unidirectional (and, in the
 first two cases, recurrent) hybridization between the widespread diploids
 D. fuchsii and D. incarnata. Differing considerably in geographical extent
 and ecological tolerance, the three allopolyploids together provide a
 useful system to explore genomic responses to allopolyploidization and
 reveal their role in adaptation to contrasting environments. Results:
 Analyses of cDNA-AFLPs show a significant increase in the range of gene
 expression of these allopolyploid lineages, demonstrating higher potential
 for phenotypic plasticity than shown by either parent. Moreover,
 allopolyploid individuals express significantly more gene variants
 (including novel alleles) than their parents, providing clear evidence for
 an increase in biological complexity following allopolyploidization.
 Significantly more genetic mutations have accumulated in the older D.
 majalis compared with the younger D. traunsteineri since their respective
 formation. Conclusions: Multiple origins of these tetraploids contribute
 to differential patterns of gene expression with a distinct geographic
 structure. However, several transcripts conserved within each
 allopolyploid taxon differ between taxa, indicating that habitat
 preferences shape similar expression patterns in these independently
 formed allopolyploids. Statistical signals separate several adaptive
 transcripts, related mainly to a combination of water availability and
 temperature that may play a role favouring the persistence of individuals
 in their native environments. In addition to stabilizing the allopolyploid
 genome, genetic and epigenetic alterations are key determinants of the
 adaptive success of the new polyploid species after recurrent
 allopolyploidization events, potentially triggering reproductive isolation
 between the resulting lineages.
description: cDNA_DactylorhizacDNA-AFLP data on diploid and polyploid individuals of Dactylorhiza
DOI: 10.15468/dl.rsjy3r
title: Occurrence Download

description: A dataset containing 9798 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Machine Observation, Human Observation, Material sample, Specimen)",
 {
 "or" : [
 "Geometry POLYGON((-74.66652 4.24186,-73.1692 4.24186,-73.1692 7.22119,-74.66652 7.22119,-74.66652 4.24186))",
 "Geometry POLYGON((-79.35145 -3.32421,-66.72148 -3.32421,-66.72148 11.50489,-79.35145 11.50489,-79.35145 -3.32421))"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Hydrochoerus hydrochaeris"
 ]
}

 The dataset includes 9798 records from 137 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000958-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.71789/qbpm-x440
title: #BLOCKED!

description: llllll
DOI: 10.5061/dryad.gr6b8
title: Data from: Molecular characterization of sexual diversity in a population of Serpula lacrymans, a tetrapolar basidiomycete

description: Different mating systems have evolved in the fungal kingdom, including a
 tetrapolar multiallelic mating system in many basidiomycetes. In
 tetrapolar species, the presence of different alleles at two mating loci
 (MAT A and MAT B) is necessary for mating to occur. The tetrapolar fungus
 Serpula lacrymans causes wood-decay in buildings in temperate regions
 worldwide and is present in Europe with a genetically homogeneous founder
 population. Using genome sequence data, we annotated the two mating type
 loci for S. lacrymans and found the expected synteny with other
 basidiomycetes, except for a retrotransposon being present in one locus
 (MAT A). We developed markers linked to the MAT A and MAT B regions and
 used these to investigate the mating type diversity in the European
 population. Moreover, we found a good match between the genetic markers
 and functional mating types as revealed by segregation and mating studies.
 A low diversity of mating types is present in the European S. lacrymans
 population caused by the founder event where a limited number of genotypes
 were introduced. This finding contrasts the situation in natural fungal
 populations where a high diversity of mating types is normally present.
 Although S. lacrymans has a large and viable population in Europe, we
 argue that the low mating type diversity restrains the dispersal and
 establishment of the fungus.
description: Dryad_readmeInformation about the Dryad accession.Dryad_alignmentAlignment of the sequence data (a part of the homeodomain transcription factor 2, HD2)Dryad_informationInformation about the analysed isolates of Serpula lacrymans.
DOI: 10.5061/dryad.21s8j
title: Data from: Is bigger better? The relationship between size and reproduction in female Asian elephants

description: The limited availability of resources is predicted to impose trade-offs
 between growth, reproduction and self-maintenance in animals. However,
 although some studies have shown that early reproduction suppresses
 growth, reproduction positively correlates with size in others. We use
 detailed records from a large population of semi-captive elephants in
 Myanmar to assess the relationships between size (height and weight),
 reproduction and survival in female Asian elephants, a species
 characterized by slow, costly life history. Although female height gain
 during the growth period overlapped little with reproductive onset in the
 population, there was large variation in age at first reproduction and
 only 81% of final weight had been reached by peak age of reproduction at
 the population level (19 years). Those females beginning reproduction
 early tended to be taller and lighter later in life, although these trends
 were not significant. We found that taller females were more likely to
 have reproduced by a given age, but such effects diminished with age,
 suggesting there may be a size threshold to reproduction which is
 especially important in young females. Because size was not linked with
 female survival during reproductive ages, the diminishing effect of height
 on reproduction with age is unlikely to be due to biased survival of
 larger females. We conclude that although reproduction may not always
 impose significant costs on growth, height may be a limiting factor to
 reproduction in young female Asian elephants, which could have important
 implications considering their birth rates are low and peak reproduction
 is young – 19 years in this population.
description: Reproductive data of
 female Asian elephantsThis data includes
 repeated height (cm) and weight (kg) measures of 150 individuals,
 identified by an ID number, with recorded age at measurement, and
 reproductive data. This reproductive data includes reproductive status at
 the age of measurement, and the number of calves born to a female and
 survived to the age of 5. This also includes their 5 year birth cohort,
 birth origin (1=wild caught, 0=captive born), and age at capture if wild
 caught (captive born age at capture=0)reproduction_dryad.csvSurvival of female Asian elephantThis data includes height (cm) measures of 104 female Asian elephants aged 20-50, along with their censorship status (1=dead, 0=alive), and their age at censorship or death. This also includes their reproductive status, their birth origin (1=wild caught, 0=captive born), and their age at capture if they are wild caught (captive born age at capture= 0).survival_data_dryad.csv
DOI: 10.5061/dryad.28kh9
title: Data from: Fire-induced population reduction and landscape opening increases gene flow via pollen dispersal in Pinus halepensis

description: Population reduction and disturbances may alter dispersal, mating patterns
 and gene flow. Rather than taking the common approach of comparing
 different populations or sites, here we studied gene flow via
 wind-mediated effective pollen dispersal on the same plant individuals
 before and after a fire-induced population drop, in a natural stand of
 Pinus halepensis. The fire killed 96% of the pine trees in the stand and
 cleared the vegetation in the area. Thirteen trees survived in two groups
 separated by ~80 m, and seven of these trees had serotinous (closed)
 pre-fire cones that did not open despite the fire. We analyzed pollen from
 closed pre- and post-fire cones using microsatellites. The two groups of
 surviving trees were highly genetically differentiated, and the pollen
 they produced also showed strong among-group differentiation and very high
 kinship both before and after the fire, indicating limited and very local
 pollen dispersal. The pollen not produced by the survivors also showed
 significant pre-fire spatial genetic structure and high kinship,
 indicating mainly within-population origin and limited gene flow from
 outside, but became spatially homogeneous with random kinship after the
 fire. We suggest that post-fire gene flow via wind-mediated pollen
 dispersal increased by two putative mechanisms: 1) a drastic reduction in
 local pollen production due to population thinning, effectively increasing
 pollen immigration; 2) an increase in wind speeds in the vegetation-free
 post-fire landscape. This research shows that dispersal can alleviate
 negative genetic effects of population size reduction, and that
 disturbances might enhance gene flow, rather than reduce it.
description: Trees, seeds and pollen
 genotypic dataDryad-Shohami&Nathan.txt
DOI: 10.5061/dryad.27m7h
title: Data from: Go big or go fish: morphological specializations in carnivorous bats

description: Specialized carnivory is relatively uncommon across mammals, and bats
 constitute one of the few groups in which this diet has evolved multiple
 times. While size and morphological adaptations for carnivory have been
 identified in other taxa, it is unclear what phenotypic traits
 characterize the relatively recent evolution of carnivory in bats. To
 address this gap, we apply geometric morphometric and phylogenetic
 comparative analyses to elucidate which characters are associated with
 ecological divergence of carnivorous bats from insectivorous ancestors,
 and if there is morphological convergence among independent origins of
 carnivory within bats, and with other carnivorous mammals.We find that
 carnivorous bats are larger and converged to occupy a subset of the
 insectivorous morphospace, characterized by skull shapes that enhance bite
 force at relatively wide gapes. Piscivorous bats are morphologically
 distinct, with cranial shapes that enable high bite force at narrow gapes,
 which is necessary for processing fish prey. All animal-eating species
 exhibit positive allometry in rostrum elongation with respect to skull
 size, which could allow larger bats to take relatively larger prey. The
 skull shapes of carnivorous bats share similarities with generalized
 carnivorans, but tend to be more suited for increased bite force
 production at the expense of gape, when compared with specialized
 carnivorans.
description: GPA
 batsAverage coordinates and
 centroid sizes from Generalized Procrustes Analysis of bats in each of the
 skull views (cranium ventral, cranium lateral, and mandible lateral).
 Values were averaged across individuals for each
 species.Bats.zipGPA Bats & CarnivoransAverage coordinates and centroid sizes from Generalized Procrustes Analysis of bats and carnivorans in each of the skull views (cranium ventral, cranium lateral, and mandible lateral). Values were averaged across individuals for each species.Bats&Carnivorans.zip
DOI: 10.5061/dryad.8265h
title: Data from: Commensalism facilitates gene flow in mountains: a comparison between two Rattus species

description: Small mammal dispersal is strongly affected by geographical barriers.
 However, commensal small mammals may be passively transported over large
 distances and strong barriers by humans (often with agricultural
 products). This pattern should be especially apparent in topographically
 complex landscapes, such as mountain ranges, where valleys and/or peaks
 can limit dispersal of less vagile species. We predict that commensal
 species would have lower genetic differentiation and higher migration
 rates than related non-commensals in such landscapes. We contrasted
 population genetic differentiation in two sympatric Rattus species (R.
 satarae and R. rattus) in the Western Ghats mountains in southern India.
 We sampled rats from villages and adjacent forests in seven locations
 (20–640 km apart). Capture-based statistics confirmed that R. rattus is
 abundant in human settlements in this region, whereas R. satarae is
 non-commensal and found mostly in forests. Population structure analyses
 using ~970-bp mitochondrial control region and 17 microsatellite loci
 revealed higher differentiation for the non-commensal species (R. satarae
 F-statistics=0.420, 0.065, R. rattus F-statistics=0.195, 0.034;
 mitochondrial DNA, microsatellites, respectively). Genetic clustering
 analyses confirm that clusters in R. satarae are more distinct and less
 admixed than those in R. rattus. R. satarae shows higher slope for
 isolation-by-distance compared with R. rattus. Although mode of migration
 estimates do not strongly suggest higher rates in R. rattus than in R.
 satarae, they indicate that migration over long distances could still be
 higher in R. rattus. We suggest that association with humans could drive
 the observed pattern of differentiation in the commensal R. rattus,
 consequently impacting not only their dispersal abilities, but also their
 evolutionary trajectories.
description: Microsatellite
 genotypesThis file contains raw
 genotypes for 17 microsatellite loci for two species of Rattus- R. rattus
 and R. satarae sampled in seven locations in Western
 Ghats.dryad.xlsx