cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18393987
title: Data and code for: Dynamic transposable element expression during Hydra head regeneration

description: Bash shell scripts for repeat modeler, masker, and STAR mapping.

Custom script to keep class_id from repeat masker output (rmOUT_to_gtf.awk)

Custom script to merge counts (R_script_merge_counts)

Counts table including all genes and TEs used for analysis (tsv table)

R script includes DDseq analysis, pairwise 12h comparisons, volcano plots, and heatmap code (Hydra_DDEseq_TE.r)
DOI: 10.5281/zenodo.18393988
title: Data and code for: Dynamic transposable element expression during Hydra head regeneration

description: Bash shell scripts for repeat modeler, masker, and STAR mapping.

Custom script to keep class_id from repeat masker output (rmOUT_to_gtf.awk)

Custom script to merge counts (R_script_merge_counts)

Counts table including all genes and TEs used for analysis (tsv table)

R script includes DDseq analysis, pairwise 12h comparisons, volcano plots, and heatmap code (Hydra_DDEseq_TE.r)
DOI: 10.5061/dryad.dfn2z34wb
title: Interspecific competition in bats and diet shifts in response to White-Nose Syndrome

description: Since the introduction of white-nose syndrome (WNS) in North America,
 numerous species of bat have dwindled in numbers. These declines observed
 are often species-specific and thus provides opportunity for a natural
 experiment to test for shifts in diet through relaxed resource
 partitioning in bat communities post-introduction of WNS. Acoustic
 monitoring at locations in Southern Ontario pre- (2009– 2011) and post-WNS
 (2012–2014) introduction showed an increase in activity of big brown bats
 (Eptesicus fuscus) corresponding to a decline in the activity of little
 brown bats (Myotis lucifugus). Next-generation sequencing of bat stomachs
 and guano in Southern Ontario before and after WNS allowed for the
 characterization of diet changes of these species. Post-WNS, E. fuscus
 consumed a wider breadth of prey and many of the insect species once
 consumed by M. lucifugus, including several pest insects. These results
 suggest that the introduction of WNS has resulted in relaxed interspecific
 competition within these bat communities in Southern Ontario.
DOI: 10.5061/dryad.hdr7sqvcs
title: Flies exploit predictable perspectives and backgrounds to enhance iridescent signal salience and mating success

description: Communication requires both the encoding of information and its effective
 transmission, but little is known about display traits that primarily
 serve to enhance efficacy. Here we examined the visual courtships
 of Lispe cana, a cursorial fly that lives and mates in
 heterogeneous foreshores, and tested the prediction that males should seek
 to enhance signal salience and consequent fitness through the flexible
 choice of display locations. We show that courting males access the field
 of view of females by straddling them and holding their wings closed,
 before moving ahead to present their structurally coloured faces in
 ritualised dances. Males preferentially present these UV-white signals
 against darker backgrounds, and the magnitude of contrast predicts female
 attention, which in turn predict mating success. Our results demonstrate a
 striking interplay between the physical and attentional manipulation of
 receivers and reveal novel routes to the enhancement of signal efficacy in
 noisy environments.
DOI: 10.5061/dryad.fn2z34tpr
title: Data from: Female solo song and duetting are associated with different territoriality in songbirds

description: Recently, there has been an increased effort to unravel selective factors
 behind female song evolution in songbirds. Female birds which produce
 songs may sing either solo or in duets; although the two vocal
 performances likely evolved through different selection forces and
 mechanisms, the majority of large-scale studies to date have focused only
 on duetting or female song in general (pooling female solo song and
 duetting into a single category). Hence, here we estimate the effect of
 behavioral life-history traits (territoriality, social bonds, cooperative
 breeding) and environmental productivity on the occurrence of female solo
 song and duetting separately in songbirds of South Africa and Lesotho. The
 focal region is characterized by subtropical/tropical climate, clear
 spatial environmental productivity gradient, and detailed knowledge on
 avian species distribution and behavioral life-history traits.
 Phylogenetically informed comparative analyses revealed that species where
 females produce only solo songs exhibited higher levels of territoriality
 than species with non-singing females (in an univariable model) but,
 simultaneously, lower levels than duetting species. Although both species
 with female solo song and duetting establish mainly long-term social
 bonds, the former defend their territories seasonally while the latter
 exhibit mainly year-round territoriality. Cooperative breeding and
 environmental productivity was not associated with the distribution of
 female solo song and duetting in any model. Our results indicate that when
 exploring female song ecology and evolution, female solo song and duetting
 are likely to be distinct song categories associated with different levels
 of territoriality.
DOI: 10.5061/dryad.xpnvx0kb4
title: Data from: Factors that can affect the spatial positioning of large and small individuals in clusters of sit-and-wait predators

description: Shadow competition, the interception of prey by sit-and-wait predators
 closest to the source of prey arrival, is prevalent in clusters of
 sit-and-wait predators. Peripheral positions in the cluster receive more
 prey and should thus be more frequently occupied. Models predicting
 spatial positioning in groups, however, usually ignore variability among
 group members. Here, I used a simulation model to determine conditions
 under which small and large sit-and-wait predators, which differ in their
 attack range, should differ in their spatial positions in the cluster.
 Small predators occupied peripheral positions more frequently than large
 predators at the simulation beginning, while the opposite held true as
 time advanced. Due to the large and small attack range of large and small
 predators respectively, small predators mistakenly relocated away from
 peripheral positions, while large predators did not relocate fast enough
 from inferior central positions. Any factor that moderated the frequent
 relocations of small predators or had the opposite effect on large
 predators assisted small or large predators respectively to reach the more
 profitable peripheral positions. Furthermore, any factor elevating shadow
 competition led to longer occupation of the periphery by large predators.
 This model may explain why sit-and-wait predators are not homogenously
 distributed in space according to size.
DOI: 10.5061/dryad.vhhmgqnpn
title: Color preference of the spotted wing Drosophila, Drosophila suzukii

description: Drosophila suzukii Matsumura (Diptera: Drosophilidae) is a significant
 invasive pest in soft-skin fruits and berries in Asia, Europe, and North
 and South America. Many herbivorous insects use multiple cues for host
 selection, particularly olfactory and visual stimuli. The visual system of
 closely-related Drosophila melanogaster is well-documented, expressing
 strong sensitivity to short-wavelength colors (ultraviolet to green) and
 only limited sensitivity to long-wavelength colors (red to infrared). Our
 results suggest that D. suzukii have limited ability to distinguish red
 consistent with visual sensitivity range within the melanogaster subgroup.
 We propose that color contrast rather than color appearance may be of
 greater importance in orientation and attraction. We propose that
 differences in reflectance between light wavelengths important for color
 opponency are key to color discrimination to provide color contrast
 between foreground and background, as occurs between fruit and foliage,
 during host-finding.
DOI: 10.5061/dryad.f4qrfj6s1
title: Data from: Differences in epiphyte biomass and community composition along landscape and within-crown spatial scales

description: Vascular epiphytes contribute to the structural, compositional, and
 functional complexity of tropical montane cloud forests because of their
 high biomass, diversity, and ability to intercept and retain water and
 nutrients from atmospheric sources. However, human-caused climate change
 and forest-to-pasture conversion are rapidly altering tropical montane
 cloud forests. Epiphyte communities may be particularly vulnerable to
 these changes because of their dependence on direct atmospheric inputs and
 host trees for survival. In Monteverde, Costa Rica, we measured vascular
 epiphyte biomass, community composition, and richness at two spatial
 scales: (1) along an elevation gradient spanning premontane forests to
 montane cloud forests; and (2) within trees along branches from inner to
 outer crown positions. We also compared epiphyte biomass and distribution
 at these scales between two different land-cover types, comparing trees in
 closed canopy forest to isolated trees in pastures. An ordination of
 epiphyte communities at the level of trees grouped forested sites above
 versus below the cloud base, and separated forest versus pasture trees.
 Species richness increased with increasing elevation and decreased from
 inner to outer branch positions. Although richness did not differ between
 land-cover types, there were significant differences in community
 composition. The variability in epiphyte community organization between
 the two spatial scales and between land-cover types underscores the
 potential complexity of epiphyte responses to climate and land-cover
 changes.
DOI: 10.5061/dryad.dr7sqv9tv
title: Data from: Genetic switches designed for eukaryotic cells and controlled by serine integrases

description: Recently, new serine integrases have been identified, increasing the
 possibility of scaling up genomic modulation tools. Here, we describe the
 use of unidirectional genetic switches to evaluate the functionality of
 six serine integrases in different eukaryotic systems: the HEK 293T cell
 lineage, bovine fibroblasts and plant protoplasts. Moreover, integrase
 activity was also tested in human cell types of therapeutic interest:
 peripheral blood mononuclear cells (PBMCs), neural stem cells (NSCs) and
 undifferentiated embryonic stem (ES) cells. The switches were composed of
 plasmids designed to flip two different genetic parts driven by serine
 integrases. Cell-based assays were evaluated by measurement of EGFP
 fluorescence and by molecular analysis of attL/attR sites formation after
 integrase functionality .Our results demonstrate that all the integrases
 were capable of inverting the targeted DNA sequences, exhibiting distinct
 performances based on the cell type or the switchable genetic sequence.
 These results should support the development of tunable genetic circuits
 to regulate eukaryotic gene expression.
DOI: 10.6086/d1kd40
title: An ancient and eroded social supergene is widespread across Formica ants

description: Supergenes, clusters of tightly linked genes, play a key role in the
 evolution of complex adaptive variation. While supergenes have been
 identified in many species, we lack an understanding of their origin,
 evolution and persistence. Here, we uncover 20-40 MY of evolutionary
 history of a supergene associated with polymorphic social organization in
 Formica ants. We show that five Formica species exhibit homologous
 divergent haplotypes spanning 11 Mbp on chromosome 3. Despite the size of
 the supergene, only 142 single nucleotide polymorphisms (SNPs)
 consistently distinguish alternative supergene haplotypes across all five
 species. These conserved trans-species SNPs are localized in a small
 number of disjunct clusters that are distributed across the supergene.
 This unexpected pattern of divergence indicates that the Formica supergene
 does not follow standard models of sex chromosome evolution, in which
 distinct evolutionary strata reflect the history of an expanding region of
 suppressed recombination. We propose an alternative “eroded strata model,”
 by which clusters of conserved trans-species SNPs represent functionally
 important areas maintained by selection in the face of rare recombination
 between ancestral haplotypes. The comparison of whole genome sequences
 across 10 additional Formica species combined with a chromosome-level F.
 selysi genome assembly reveal that the most conserved region of the
 supergene contains the gene Knockout, a transcription factor essential for
 motor neuron development in Drosophila. The discovery that a very small
 portion of this large and ancient supergene harbors conserved
 trans-species SNPs linked to colony social organization suggests that the
 ancestral haplotypes have been eroded by recombination, with selection
 preserving differentiation at one or a few genes generating alternative
 social organization.
description: Linkage maps were constructed from ddRAD data for 67 males from a
 monogyne colony (F. exsecta) and 112 offspring from two F. selysi queens
 (F. selysi Sp haplotype) using MSTmap.
description: EcoRI_ddRAD_oligos: All oligonucleotides were ordered as
 unmodified DNA, with standard desalting, for use with the custom ddRAD
 protocol of Brelsford et al. 2016, Heredity, modified to use EcoRI in
 place of SbfI.
DOI: 10.5061/dryad.1zcrjdfnf
title: Data from: Testing predictions of inclusive fitness theory in inbreeding relatives with biparental care

description: Inclusive fitness theory predicts that parental care will vary with
 relatedness between potentially caring parents and offspring, potentially
 shaping mating system evolution. Systems with extra-pair paternity (EPP),
 and hence variable parent-brood relatedness, provide valuable
 opportunities to test this prediction. However, existing theoretical and
 empirical studies assume that a focal male is either an offspring’s father
 with no inbreeding, or is completely unrelated. We highlight that this
 simple dichotomy does not hold given reproductive interactions among
 relatives, complicating the effect of EPP on parent-brood relatedness yet
 providing new opportunities to test inclusive fitness theory. Accordingly,
 we tested hierarchical hypotheses relating parental feeding rate to
 parent-brood relatedness, parent kinship and inbreeding, using song
 sparrows (Melospiza melodia) experiencing natural variation in
 relatedness. As predicted, male and female feeding rates increased with
 relatedness to a dependent brood, even controlling for brood size. Male
 feeding rate tended to decrease as paternity loss increased, and increased
 with increasing kinship and hence inbreeding between socially-paired
 mates. We thereby demonstrate that variation in a key component of
 parental care concurs with subtle predictions from inclusive fitness
 theory. We additionally highlight that such effects can depend on the
 underlying social mating system, potentially generating status-specific
 costs of extra-pair reproduction.
DOI: 10.5061/dryad.s4mw6m936
title: Embryo survival in the oviduct not significantly influenced by major histocompatibility complex social signaling in the horse

description: The major histocompatibility complex (MHC) influences sexual selection in
 various vertebrates. Recently, MHC-linked social signaling was also shown
 to influence female fertility in horses (Equus caballus) diagnosed 17 days
 after fertilization. However, it remained unclear at which stage the
 pregnancy was terminated. Here we test if MHC-linked cryptic female choice
 in horses happens during the first days of pregnancy, i.e., until shortly
 after embryonic entrance into the uterus and before fixation in the
 endometrium. We exposed estrous mares to one of several unrelated
 stallions, instrumentally inseminated them with semen of another stallion,
 and flushed the uterus 8 days later to test for the presence of embryos.
 In total 68 embryos could be collected from 97 experimental trials. This
 success rate of 70.1% was significantly different from the mean pregnancy
 rate of 45.7% observed 17 days after fertilization using the same
 experimental protocol but without embryo flushing. Embryo recovery rate
 was not significantly dependent on whether the mares had been socially
 exposed to an MHC-dissimilar or an MHC-similar stallion. These
 observations suggest that MHC-linked maternal strategies affect embryo
 survival mainly (or only) during the time of fixation in the uterus.
description: See description in Jeannerat et al.
description: See description in Jeannerat et al.
DOI: 10.3886/e244689
title: Kibritçi kız

description: Kibritçi Kız
DOI: 10.5061/dryad.vq83bk3nq
title: A randomized clinical trial to compare P. falciparum gametocytaemia and infectivity following blood-stage or mosquito bite induced controlled malaria infection

description: For malaria elimination efforts, it is important to better understand
 parasite transmission to mosquitoes and to develop models to allow early
 clinical evaluation of transmission-blocking interventions. We previously
 described a Controlled Human Malaria Infection protocol for induction of
 gametocytemia in malaria naïve volunteers by mosquito bite (CHMI-trans)
 (Reuling et al., 2018).  Here, we compared gametocyte production
 and infectivity in the CHMI-trans model after bites of Plasmodium
 falciparum (Pf)- infected mosquitoes  to that after intravenous
 administration of  Pf-infected-erythrocytes.  Volunteers
 received (sub) curative treatments with gametocyte-permissive piperaquine
 or sulfadoxine-pyrimethamine. Blood-stage inoculation induced considerably
 higher gametocyte densities compared to mosquito bitesthat was predicted
 by PfAP2-G transcripts indicative of gametocyte commitment, and resulted
 in Pf-positive mosquito infections in 9/12 volunteers versus 0/12
 volunteers after mosquito bite inoculation. Current findings firmly
 establish the CHMI-trans with intravenous administration of asexual
 parasites as a model for early clinical evaluation of interventions that
 aim to interrupt Pf-transmission.
DOI: 10.5061/dryad.5tb2rbp0q
title: Pelagiella exigua, an early Cambrian stem gastropod with chaetae: lophotrochozoan heritage and conchiferan novelty

description: Exceptionally well-preserved impressions of two bundles of bristles
 protrude from the apertures of small, spiral shells of Pelagiella exigua,
 recovered from the Kinzers Formation (Cambrian, Stage 4, “Olenellus Zone”,
 ~ 512 Ma) of Pennsylvania. These impressions are inferred to represent
 clusters of chitinous chaetae, comparable to those borne by annelid
 parapodia and some larval brachiopods. They provide an affirmative test in
 the early metazoan fossil record of the inference, from phylogenetic
 analyses of living taxa, that chitinous chaetae are a shared early
 attribute of the Lophotrochozoa. Shells of Pelagiella exhibit logarithmic
 spiral growth, microstructural fabrics, distinctive external sculptures,
 and muscle scars characteristic of molluscs. Hence, Pelagiella has been
 regarded as a stem mollusc, a helcionelloid expressing partial torsion, an
 untorted paragastropod, or a fully torted basal member of the gastropod
 crown group. The inference that its chaeta-bearing appendages were
 anterior-lateral, based on their probable functions, prompts a new
 reconstruction of the anatomy of Pelagiella, with a mainly anterior mantle
 cavity. Under this hypothesis, two lateral-dorsal grooves, uniquely
 preserved in Pelagiella atlantoides, are interpreted as sites of
 attachment for a long left ctenidium and a short one, anteriorly on the
 right. The orientation of Pelagiella and the asymmetry of its gills,
 comparable to features of several living vetigastropods, nominate it as
 the earliest fossil mollusc known to exhibit evidence of the developmental
 torsion characteristic of gastropods. This key adaptation facilitated an
 evolutionary radiation, slow at first and rapid during the Ordovician that
 gave rise to the remarkable diversification of the Gastropoda.
DOI: 10.15468/dl.95r2ax
title: Occurrence Download

description: A dataset containing 761 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "TaxonKey is Canis latrans thamnos"
 ]
}

 The dataset includes 761 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002008-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.bcc2fqz7f
title: Impact of mitonuclear interactions on life-history responses to diet

description: Mitochondria are central to both energy metabolism and biosynthesis.
 Mitochondrial function could therefore influence resource allocation.
 Critically, mitochondrial function depends on interactions between
 proteins encoded by the mitochondrial and nuclear genomes. Severe
 incompatibilities between these genomes can have pervasive effects on both
 fitness and longevity. How milder deficits in mitochondrial function
 affect life-history trade-offs is less well understood. Here we analyse
 how mitonuclear interactions affect the trade-off between fecundity and
 longevity in Drosophila melanogaster. We consider a panel of 10 different
 mitochondrial DNA haplotypes against two contrasting nuclear backgrounds
 (WE and ZIM) in response to high-protein versus standard diet. We report
 strikingly different responses between the two nuclear backgrounds. WE
 females have higher fecundity and decreased longevity on high-protein. ZIM
 females have much greater fecundity and shorter lifespan than WE flies on
 standard diet. High-protein doubled their fecundity with no effect on
 longevity. Mitochondrial haplotype reflected nuclear life-history
 trade-offs, with a negative correlation between longevity and fecundity in
 WE flies and no correlation in ZIM flies. Mitonuclear interactions had
 substantial effects but did not reflect genetic distance between
 mitochondrial haplotypes. We conclude that mitonuclear interactions can
 have significant impact on life-history trade-offs, but their effects are
 not predictable by relatedness.
DOI: 10.5061/dryad.280gb5mm9
title: The influence of experimentally induced polyploidy on the relationships between endopolyploidy and plant function in Arabidopsis thaliana

description: Whole genome duplication, leading to polyploidy and endopolyploidy, occurs
 in all domains and kingdoms and is especially prevalent in vascular
 plants. Both polyploidy and endopolyploidy increase cell size, but it is
 uncertain whether both processes have similar effects on plant morphology
 and function, or whether polyploidy influences the magnitude of
 endopolyploidy. To address these gaps in knowledge, fifty-five
 geographically separated diploid genotypes (i.e., accessions) of
 Arabidopsis thaliana that span a gradient of endopolyploidy were
 experimentally manipulated to induce polyploidy. Both the diploids and
 artificially induced tetraploids were grown in a common greenhouse
 environment and evaluated with respect to nine reproductive and vegetative
 characteristics. Induced polyploidy decreased leaf endopolyploidy and stem
 endopolyploidy along with specific leaf area, stem height, but increased
 days to bolting, leaf size, leaf dry mass and leaf water content.
 Phenotypic responses to induced polyploidy varied significantly among
 genotypes but this did not affect the relationship between phenotypic
 traits and endopolyploidy. Our results provide the experimental support
 for a trade-off between induced polyploidy and endopolyploidy, which
 caused induced polyploids to have lower endopolyploidy than diploids.
 Though polyploidy did not influence the relationship between
 endopolyploidy and plant traits, phenotypic responses to experimental
 genome duplication could not be easily predicted because of strong
 cytotype by genotype interactions.