cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c2n18
title: Data from: Predator community structure and trophic linkage strength to a focal prey

description: Predator abundance and community structure can increase or decrease the
 suppression of lower trophic levels, although studies of these
 interactions under field conditions are relatively few. We investigated
 how the frequency of consumption (measured using PCR-based gut analysis)
 is affected by predator abundance, community diversity and evenness under
 realistic conditions. Soil arthropod communities in sixteen maize fields
 were measured (number of predators, diversity [Shannon H], and evenness
 [J]) and predator guts were searched for DNA of the focal subterranean
 herbivore, the corn rootworm (Diabrotica virgifera). Predator abundance
 and diversity were positively correlated with trophic linkage strength
 (the proportion positive for rootworm DNA), although the latter
 characteristic was not significantly so. The diversity and evenness of the
 predator community with chewing mouthparts was strongly correlated with
 their linkage strength to rootworms, whereas the linkage strength of
 fluid-feeding predators were unaffected by their community
 characteristics. Chewing predators are more affected by the rootworm’s
 hemolymph defense. This research clearly shows that predator abundance and
 diversity influences the strength of a community’s trophic linkage to a
 focal pest, and that these community characteristics may be particularly
 important for less palatable or protected prey species. We also make the
 case for conserving diverse and abundant predator communities within
 agroecosystems as a form of pest management.
description: Diversity Community
 & PredationData files for all the
 analyses in the manuscript
DOI: 10.5061/dryad.h2t57
title: Data from: Transcriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphic

description: Background: In Eucalyptus genus, studies on genome composition and
 transposable elements (TEs) are particularly scarce. Nearly half of the
 recently released Eucalyptus grandis genome is composed by
 retrotransposons and this data provides an important opportunity to
 understand TE dynamics in Eucalyptus genome and transcriptome. Results: We
 characterized nine families of transcriptionally active LTR
 retrotransposons from Copia and Gypsy superfamilies in Eucalyptus grandis
 genome and we depicted genomic distribution and copy number in two
 Eucalyptus species. We also evaluated genomic polymorphism and
 transcriptional profile in three organs of five Eucalyptus species. We
 observed contrasting genomic and transcriptional behavior in the same
 family among different species. RLC_egMax_1 was the most prevalent family
 and RLC_egAngela_1 was the family with the lowest copy number. Most
 families of both superfamilies have their insertions occurring &lt;3
 million years, except one Copia family, RLC_egBianca_1. Protein
 theoretical models suggest different properties between Copia and Gypsy
 domains. IRAP and REMAP markers suggested genomic polymorphisms among
 Eucalyptus species. Using EST analysis and qRT-PCRs, we observed
 transcriptional activity in several tissues and in all evaluated species.
 In some families, osmotic stress increases transcript values. Conclusion:
 Our strategy was successful in isolating transcriptionally active
 retrotransposons in Eucalyptus, and each family has a particular genomic
 and transcriptional pattern. Overall, our results show that
 retrotransposon activity have differentially affected genome and
 transcriptome among Eucalyptus species.
description: Reverse transcriptase
 sequences used for phylogenetic analysesCopia and Gypsy LTR
 Retrotransposon evolutionary lineages in Eucalyptus were attributed based
 on phylogenetic analysis of these elements. Material and Methods of the
 BMC Plant Biology details our approach.Phylogeny
 data.zip
DOI: 10.5061/dryad.c9m2d
title: Data from: Artificial bat roosts did not accelerate forest regeneration in abandoned pastures in southern Costa Rica

description: Artificial roosts have been proposed as a tool for augmenting bat
 populations and catalyzing tropical forest regeneration. In the best case
 scenario, roosts would attract seed-carrying bats (Family Phyllostomidae)
 into degraded pastures and form nucleating patches of native vegetation.
 We tested this scenario by monitoring 48 artificial roosts in pastures and
 adjacent forest fragments in southern Costa Rica over 2 years. Half of the
 pasture roosts were exposed to direct sunlight and half were affixed to
 4-m living stakes of Erythrina poeppigiana (Walp.) O.F. Cook that provided
 shade. After 2 years, 94% of roosts in forest and 40% of roosts in pasture
 had been used by bats at least once – primarily for nocturnal feeding.
 Maximum daily temperature inside of roosts was the best microclimatic
 predictor of bat visitation. We identified at least five species of bats
 that visited roosts, including two frugivores (Carollia and Glossophaga
 spp.). Bat-mediated seed dispersal increased with the number of
 frugivorous bat detections at roosts, but seedling recruitment did not
 increase with either bat detections or seed abundance over a 2-year
 period. Given that bats rarely used roosts in pastures, and bat visitation
 did not increase seedling recruitment, our data suggest that artificial
 bat roosts did not accelerate forest regeneration in abandoned, premontane
 pastures in southern Costa Rica. This method could be refined by
 investigating alternative roost designs, barriers to seedling recruitment
 below roosts, improvement of roost microclimatic conditions in pastures,
 and ability of bats to detect roosts in different habitats.
description: Artificial Bat Roost
 DataThis file includes data
 on bat detections, roost temperatures, seed rain, and seedling
 recruitment. Please see the ReadMe file and the manuscript for more
 information.
DOI: 10.15468/dl.q46z9w
title: Occurrence Download

description: A dataset containing 311 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Impatiens hawkeri",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 311 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001111-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dk034
title: Data from: Early-life inflammation, immune response and ageing

description: Age-related diseases are often attributed to immunopathology, which
 results in self-damage caused by an inappropriate inflammatory response.
 Immunopathology associated with early-life inflammation also appears to
 cause faster ageing, although we lack direct experimental evidence for
 this association. To understand the interactions between ageing,
 inflammation and immunopathology, we used the mealworm beetle Tenebrio
 molitor as a study organism. We hypothesized that phenoloxidase, an
 important immune effector in insect defence, may impose substantial
 immunopathological costs by causing tissue damage to Malpighian tubules
 (MTs; functionally equivalent to the human kidney), in turn accelerating
 ageing. In support of this hypothesis, we found that RNAi knockdown of
 phenoloxidase (PO) transcripts in young adults possibly reduced
 inflammation-induced autoreactive tissue damage to MTs, and increased
 adult lifespan. Our work thus suggests a causative link between
 immunopathological costs of early-life inflammation and faster ageing. We
 also reasoned that if natural selection weakens with age, older
 individuals should display increased immunopathological costs associated
 with an immune response. Indeed, we found that while old infected
 individuals cleared infection faster than young individuals, possibly they
 also displayed exacerbated immunopathological costs (larger decline in MT
 function) and higher post-infection mortality. RNAi-mediated knockdown of
 PO response partially rescued MTs function in older beetles and resulted
 in increased lifespan after infection. Taken together, our data are
 consistent with a direct role of immunopathological consequences of immune
 response during ageing in insects. Our work is also the first report that
 highlights the pervasive role of tissue damage under diverse contexts of
 ageing and immune response.
description: Data archiving_impact of
 ageing on immunity & immunopathology
DOI: 10.5061/dryad.80n42
title: Data from: Does the colonization of new biogeographic regions influence the diversification and accumulation of clade richness among the Corvides (Aves: Passeriformes)?

description: Regional variation in clade richness can be vast, reflecting differences
 in the dynamics of historical dispersal and diversification among
 lineages. Although it has been proposed that dispersal into new
 biogeographic regions may facilitate diversification, to date there has
 been limited assessment of the importance of this process in the
 generation, and maintenance, of broad-scale biodiversity gradients. To
 address this issue, we analytically derive biogeographic regions for a
 global radiation of passerine birds (the Corvides, c. 790 species) that
 are highly variable in the geographic and taxonomic distribution of
 species. Subsequently, we determine rates of historical dispersal between
 regions, the dynamics of diversification following regional colonization,
 and spatial variation in the distribution of species that differ in their
 rates of lineage diversification. The results of these analyses reveal
 spatiotemporal differences in the build-up of lineages across regions. The
 number of regions occupied and the rate of transition between regions both
 predict family richness well, indicating that the accumulation of high
 clade richness is associated with repeated expansion into new geographic
 areas. However, only the largest family (the Corvidae) had significantly
 heightened rates of both speciation and regional transition, implying that
 repeated regional colonization is not a general mechanism promoting
 lineage diversification among the Corvides.
description: Maximum clade
 credibility tree (789 species)Maximum clade
 credibility (MCC) phylogeny of 789 species of the Corvides as recognized
 by the IOC v.2.7. This phylogeny is based on a bayesian analyses of
 mitochondrial and nuclear DNA sequences for 665 species. The remaining 124
 species for which sequence data was unavailable were added as polytomies
 to the phylogeny based on this taxonomic knowledge, before a birth-death
 model was used to resolve the polytomies and assign branch lengths. This
 process generated a fully bifurcating tree for 789 corvoid
 species.Corvides_MCC_789.tre
DOI: 10.5061/dryad.b78g9
title: Data from: Male courtship preferences demonstrate discrimination against allopatric colour morphs in a cichlid fish

description: Whether premating isolation is achieved by male-specific, female-specific
 or sex-independent assortative preferences often depends on the underlying
 evolutionary processes. Here we test mate preferences of males presented
 with females of different allopatric colour variants of the cichlid fish
 Tropheus, a Lake Tanganyika endemic with rich geographic colour pattern
 variation, in which the strength of sexual isolation varies between
 populations. We conducted two-way mate choice experiments to compare
 behaviour of males of a red-bodied morph (population Moliro) towards
 females from their own population with behaviour towards females from four
 allopatric populations at different stages of phylogenetic and phenotypic
 divergence. Males courted same-population females significantly more
 intensely than females of other populations, and reduced their
 heteromorphic courtship efforts both with increasing genetic and
 increasing phenotypic distinctness of the females. In particular, females
 of a closely related red-bodied population received significantly more
 courtship than either genetically distinct, similarly coloured females
 (“Kirschfleck” morph) or genetically related, differently coloured females
 (“yellow-blotch” morph), both of which were courted similarly. Genetically
 and phenotypically distinct females (T. polli) were not courted at all.
 Consistent with previous female-choice experiments, female courtship
 activity also decreased with increasing genetic distance from the males’
 population. Given successful experimental and natural introgression
 between colour morphs and the pervasive allopatry of related variants, we
 consider it unlikely that assortative preferences of both sexes were
 driven by direct selection during periods of secondary contact or, in
 turn, drove colour pattern differentiation in allopatry. Rather, we
 suggest that sexual isolation evolved as by-product of allopatric
 divergence.
description: Tropheus moorii male
 courtship data
DOI: 10.5061/dryad.v2s71
title: Data from: Attraction, oviposition and larval survival of the fungus gnat, Lycoriella ingenua, on fungal species isolated from adults, larvae, and mushroom compost

description: We previously showed that the females of the mushroom sciarid, Lycoriella
 ingenua (Dufour, 1839) (Diptera: Sciaridae), one of the most severe pests
 of the cultivated white button mushroom, Agaricus bisporus (J.E. Lange)
 Emil J. Imbach (Agaricales: Agaricaceae), are attracted to the mushroom
 compost that mushrooms are grown on and not to the mushrooms themselves.
 We also showed that females are attracted to the parasitic green mold,
 Trichoderma aggressivum. In an attempt to identify what is in the mushroom
 compost that attracts female L. ingenua, we isolated several species of
 fungi from adult males and females, third instar larvae, and mushroom
 compost itself. We then analyzed the attraction of females to these
 substrates using a static-flow two choice olfactometer, as well as their
 oviposition tendencies in another type of assay under choice and no-choice
 conditions. We also assessed the survival of larvae to adulthood when
 first instar larvae were placed on each of the isolated fungal species. We
 found that female flies were attracted most to the mycoparasitic green
 mold, T. aggressivum, to Penicilium citrinum isolated from adult female
 bodies, and to Scatylidium thermophilium isolated from the mushroom
 compost. Gravid female flies laid the most eggs on T. aggressivum,
 Aspergillus flavus isolated from third instar larval frass, Aspergillus
 fumigatus isolated from adult male bodies, and on P. citrinum. This
 egg-laying trend remained consistent under no-choice conditions as females
 aged. First instar larvae developed to adulthood only on S. thermophilium
 and Chaetomium sp. isolated from mushroom compost, and on P. citrinum. Our
 results indicate that the volatiles from a suite of different fungal
 species act in tandem in the natural setting of mushroom compost, with
 some first attracting gravid female flies and then others causing them to
 oviposit. The ecological context of these findings is important for
 creating an optimal strategy for using possible semiochemicals isolated
 from these fungal species to better monitor and control this pestiferous
 mushroom fly species.
description: Raw
 DataHere we provide the raw
 data for each figure.
DOI: 10.5061/dryad.54fk2
title: Data from: Pathways of cryptic invasion in a fish parasite traced using coalescent analysis and epidemiological survey

description: Introduced species have the potential to outperform natives via the
 introduction of new parasites to which the native ecosystem is vulnerable.
 Cryptic diversity within an invasive species can obscure invasion patterns
 and confound proper management measures. The aim of this study is to use
 coalescent theory based methodology to trace recent routes of invasion in
 populations of Ligula intestinalis, a globally distributed fish parasite
 possessing both native and recently introduced populations in North
 Africa. Molecular analyses of mitochondrial DNA discerned a pronounced
 genetic divergence between introduced and native populations. Distribution
 of mitochondrial haplotypes demonstrated common origin of European
 populations with North African parasites sampled from introduced fish
 species in Tunisia. To test the suggested pathway of introduction,
 microsatellite data were examined in a model-based coalescent analysis
 using the software MIGRATE, where Europe to Tunisia direction of migration
 was favoured over alternative hypotheses of gene flow. Specificity of
 Tunisian populations to different host species was assessed in an
 epidemiologic survey confirming prevailing host-based division between
 introduced and native parasites in North Africa. This approach combining
 advanced analysis of molecular markers with host-specificity data allows
 revealing the evolution of host-parasite interactions following biological
 invasion and provides basis for devising future management measurements.
description: Microsatellite data for
 Ligula intestinalis from Europe and TunisiaMigrateEU_TNpop.txtMicrosatellite data for Ligula intestinalis from France and TunisiaMigrateFr_TNpop.txtMicrosatellite data for Ligula intestinalis from Czechia and TunisiaMigrateCZ_TNpop.txt
DOI: 10.5061/dryad.nk4m0
title: Data from: A new multiplex SNP genotyping assay for detecting hybridization and introgression between the M and S molecular forms of Anopheles gambiae

description: The M and S forms of A. gambiae have been the subject of intense study,
 but are morphologically indistinguishable and can only be identified using
 molecular techniques. PCR-based assays to distinguish the two forms have
 been designed and applied widely. However, the application of these assays
 towards identifying hybrids between the two forms, and backcrossed hybrids
 in particular, has been problematic as the currently available diagnostic
 assays are based on single loci, and/or are located within a multi-copy
 gene. Here we present an alternative genotyping method for detecting
 hybridization and introgression between M and S molecular forms based on a
 multi-locus panel of single nucleotide polymorphisms (SNPs) fixed between
 the M and S forms. The panel of SNPs employed are located in so called
 “islands of divergence” leading us to describe this method as the
 “Divergence Island SNP” (DIS) assay. We show this multi-locus SNP
 genotyping approach can robustly and accurately detect F1 hybrids as well
 as backcrossed individuals.
description: DIS genotype
 dataDivergence Island SNP
 genotype data for each individual isolates from four sites (Kondi,
 Foumbot, Tiko and Abu).SNPdata_Placeholder.txt
DOI: 10.5061/dryad.bj8ck
title: Data from: Morphological change and phenotypic plasticity in native and non–native pumpkinseed sunfish in response to sustained water velocities

description: Phenotypic plasticity can contribute to the proliferation and invasion
 success of nonindigenous species by promoting phenotypic changes that
 increase fitness, facilitate range expansion and improve survival. In this
 study, differences in phenotypic plasticity were investigated using
 young-of-year pumpkinseed sunfish from colonies established with lentic
 and lotic populations originating in Canada (native) and Spain
 (non-native). Individuals were subjected to static and flowing water
 treatments for 80 days. Inter- and intra-population differences were
 tested using ancova and discriminant function analysis, and differences in
 phenotypic plasticity were tested through a manova of discriminant
 function scores. Differences between Iberian and North American
 populations were observed in dorsal fin length, pectoral fin position and
 caudal peduncle length. Phenotypic plasticity had less influence on
 morphology than genetic factors, regardless of population origin. Contrary
 to predictions, Iberian pumpkinseed exhibited lower levels of phenotypic
 plasticity than native populations, suggesting that canalization may have
 occurred in the non-native populations during the processes of
 introduction and range expansion.
description: Yavno_Fox_DATARaw morphological measurements of traits associated with both the traditional centroid, and swimming. Trait names are listed at the top of each column; population and water treatment are listed in the first two columns.
DOI: 10.5061/dryad.rs046
title: Data from: Mitochondrial genetic structure and matrilineal origin of white sharks, Carcharodon carcharias, in the Northeastern Pacific: implications for their conservation

description: White sharks (Carcharodon carcharias, WS henceforth) are globally and
 regionally threatened. Understanding their patterns of abundance and
 connectivity, as they relate to habitat use, is central for delineating
 conservation units and identifying priority areas for conservation. We
 analyzed mitochondrial data to test the congruence between patterns of
 genetic connectivity and of individual movements in the Northeastern
 Pacific (NEP) and to trace the matrilineal origin of immature WS from
 coastal California and Baja California to adult aggregation areas. We
 analyzed 186 mitochondrial control region sequences from sharks sampled in
 Central California (CC; n = 61), Southern California Bight (SCB; n = 25),
 Baja California Pacific coast (BCPC; n = 9), Bahía Vizcaíno (BV; n = 39),
 Guadalupe Island (GI; n = 45), and the Gulf of California (GC; n = 7).
 Significant mitochondrial differentiation between adult aggregation areas
 (CC, GI) revealed two reproductive populations in the NEP. We found
 general concordance between movement patterns of young and adult WS with
 genetic results. Young sharks from coastal California and Baja California
 were more likely born from females from GI. Mitochondrial differentiation
 of young-of-the-year from SCB and BV suggests philopatry to nursery areas
 in females from GI. These results provide a genetic basis of female
 reproductive behavior at a regional scale and point to a preponderance of
 sharks from GI in the use of the sampled coastal region as pupping
 habitat. These findings should be considered in Mexican and US management
 and conservation strategies of the WS NEP population.
description: White shark Haplotype
 Sequences from Northeastern PacificNucleotide alignment of
 Control Region haplotype sequences of white shark from Northeastern
 PacificOnate-Gonzalez_etal_JOF-2015-051_Haplotype sequences.nex