cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4f4qrfjbv
title: Recent activity in expanding populations and purifying selection have shaped transposable element landscapes across natural accessions of the Mediterranean grass Brachypodium distachyon

description: Transposable element (TE) activity has emerged as a major cause of
 variation in genome size and structure among species. To what extent TEs
 contribute to genetic variation and divergence within species, however, is
 much less clear, mainly because population genomic data have so far only
 been available for the classical model organisms. In this study, we use
 the annual Mediterranean grass Brachypodium distachyon to investigate TE
 dynamics in natural populations. Using whole-genome sequencing data for 53
 natural accessions, we identified more than 5,400 TE polymorphisms across
 the studied genomes. We found, first, that while population bottlenecks
 and expansions have shaped genetic diversity in B. distachyon, these
 events did not lead to lineage-specific activations of TE families, as
 observed in other species. Instead, the same families have been active
 across the species range and TE activity is homogeneous across
 populations, indicating the presence of conserved regulatory mechanisms.
 Second, almost half of the TE insertion polymorphisms are
 accession-specific, most likely because of recent activity in expanding
 populations and the action of purifying selection. And finally, although
 TE insertion polymorphisms are underrepresented in andaroundgenes,more
 than 1,000 of them occur in genic regions and could thus contribute to
 functional divergence. Our study shows that while TEs in B. distachyon are
 “well-behaved”compared with TEs in other species with larger genomes, they
 are an abundant source of lineage-specific genetic variation and may play
 an important role in population divergence and adaptation.
description: The genomes of the 53 B. distachyon accessions analyzed in this
 study were recently sequenced at a mean coverage of 74 to create a B.
 distachyon pan-genome (supplementary table S1, Supplementary Material
 online; Gordon et al. 2017). For each accession, we aligned the 76 or
 100bp Illumina paired- end reads with BWA-MEM (standard settings, Li 2013)
 to version 2.0 of the B. distachyon reference genome. After removing
 duplicates with Sambamba (Tarasov et al. 2015), single nucleotide
 polymorphisms were called with Freebayes (Garrison and Marth 2012).
 Standard settings were used for both programs. The following filters were
 applied to the raw Freebayes output: we first removed indels and variants
 in low complexity regions identified with Dustmasker (Morgulis et al.
 2006). VCFtools v0.1.12b (Danecek et al. 2011) was then used to remove
 SNPs with a quality lower than 30 and amean depth lower than half or
 higher than twice the genome-wide average depth at all variant sites. This
 filtered data set with 5,918,789 SNPs will be referred to as the full SNP
 data set; further filtering steps were adapted to the requirements of the
 different meth- ods and are described below.
DOI: 10.5061/dryad.3n5tb2rh3
title: Lacistorhynchidae family 28S alignment

description: Aim: Trypanorhyncha cestodes comprise a wide range of heteroxenous
 parasites infecting elasmobranchs as definitive hosts, with crustaceans,
 squids, and fishes acting as intermediate/paratenic hosts. Limited data
 exist on the larval infection of these cestodes and the role of
 intermediate and paratenic hosts in the life cycle of these parasites. In
 this study, we investigated the factors that determine the occurrence and
 the level of infection of Grillotia plerocerci in the skeletal muscles of
 various deep sea benthonic sharks and analysed the parasites through an
 integrative taxonomic approach. Location: Gulf of Naples, Mediterranean
 Sea. Methods: Sharks obtained as bycatch of commercial trawling activities
 (i.e., Etmopterus spinax, Galeus melastomus and Scyliorhinus canicula)
 were used in this study. Data from a limited number of Dalatias licha and
 Scyliorhinus stellaris were also included. Grillotia plerocerci were
 molecularly characterized using the partial 28S large subunit rDNA.
 Boosted regression trees were used to model the relationship between the
 abundance of infection with both morphological and physiological
 predictors in each host. Results: Plerocerci of Grillotia were detected in
 all shark species except S. stellaris. Host species significantly differed
 in terms of parasite abundance, with the highest and lowest prevalence and
 abundance of infection detected in G. melastomus and E. spinax,
 respectively. The relative influence of the traits involved in explaining
 the parasite abundance were related to the host size in G. melastomus,
 while both morphology- and physiology-related traits (e.g., gonadosomatic
 and hepatosomatic indices) explained the patterns observed in E. spinax
 and S. canicula. The 28S rDNA sequences shared identity of ∼99.40% with a
 Grillotia species previously found in the Mediterranean Sea. At
 intraspecific level, two different genotypes were found. A first type was
 retrieved only from D. licha, whereas a second type was found in G.
 melastomus, E. spinax, and S. canicula. Main conclusions: Present results
 suggest that the two genotypes could be involved in different
 consumer-resource systems and confirm most of the examined shark species
 as transport hosts of Grillotia species for unknown larger top predators.
DOI: 10.5061/dryad.59zw3r26r
title: Data from: Indigenous knowledge of key ecological processes confers resilience to a small-scale kelp fishery

description: 1. Feedbacks between social and ecological processes can lead to
 sustainable stewardship practices that support ecological resilience among
 harvested populations. This is evident along the world’s coast lines,
 where Indigenous knowledge systems have facilitated millennia of human
 nature coexistence. However, social-ecological conditions globally are
 quickly shifting, posing challenges for coastal Indigenous communities
 where customary harvest of ocean resources, such as kelps, need to adapt
 to growing markets, novel climates and changing governance regimes.
 Consequently, a pressing need exists to determine how specific ecological
 and social variables drive key dynamics within coupled human-ocean
 systems. 2. Motivated by the information needs of an Indigenous community
 on Canada’s Pacific Coast, we co-designed a traditional harvest
 experiment, field surveys, and semi-directed interviews with Indigenous
 resource users and managers to measure the ecological resilience of the
 feather boa kelp (Egregia menziesii) to harvest and determine what
 environmental variables most affected its recovery. We wove these results
 with information on current stewardship practices to inform future
 management of this slow growing perennial kelp based on Indigenous
 knowledge and western science. 3. We found that Egregia recovered from
 traditional harvest levels faster than expected with minimal impact on its
 productivity because plants sprouted new fronds. In fact, traditional
 harvest levels of Egregia mimicked natural frond loss. Indigenous
 knowledge and empirical ecological evidence revealed the importance of
 individual plant size, site-specific seawater temperature and wave
 exposure in driving Egregia recovery. Indigenous stewardship practices
 reflected these ecological relationships in the practice of selecting
 large plants from sites with healthy patches of Egregia. While we
 documented key social controls of harvest, current self-reported harvest
 levels of kelp fronds were 2 times greater than the stated social norm,
 but only 1.2 times greater in terms of kelp biomass. 4. Consequently,
 traditional harvest protocols facilitate Egregia recovery and promote its
 sustained use. However, its ecological resilience is susceptible to the
 erosion of customary practices and warming ocean temperatures. 5.
 Co-produced research that mobilizes multiple bodies of knowledge can
 enhance our understanding of social-ecological resilience, empower local
 decision makers, and democratize the science and practice of natural
 resource management.
description: Experimental harvest of <em>Egregia
 menziesii</em> This data includes kelp growth
 metrics in response to harvest treatment as well as site specific
 environmental conditions. These data can be used to create the glms
 presented in the paper. Please see READme for a short description of the
 data and description of data elements.
DOI: 10.5061/dryad.bcc2fqzc3
title: A sexual dimorphism in the spatial vision of North American band-winged grasshoppers

description: Visual acuity (VA) --- a measurement of the fineness or coarseness of
 vision --- may vary within a species including between the biological
 sexes. Although numerous studies have found males with finer VA than
 females, relatively few have shown the opposite with females having finer
 vision. This is surprising because our understanding of between species
 differences in VA suggests that females may have finer vision than males
 if they 1) are larger than males, or 2) need finer vision to detect and/or
 discriminate between males. Here, we estimate the interommatidial angle
 (∆Φ, an anatomical measurement of VA) in three species of band-winged
 grasshoppers in which females are both the larger sex and likely interpret
 visual signals (Arphia pseudonietana, Dissosteira carolina, and
 Spharagemon equale; total n = 98). Using a radius of curvature estimation
 method, we find that females have ~19% finer estimated ∆Φ than males in
 the most acute region and axis of the eye, but that this dimorphism varies
 between species. Further visual explorations of the species showing the
 greatest body size dimorphism (D. carolina) suggest that this ∆Φ
 dimorphism is driven by females having larger eyes with more ommatidia. In
 contrast to many diurnal flying insects where males have finer vision to
 acquire mates, our study is one of the first to demonstrate a
 female-biased sexual dimorphism in acuity. Given 1) the number of species
 in which females are larger than males, and 2) the variability of mating
 behaviors across taxa, our results suggest that differences in VA between
 the sexes may be more common than currently appreciated.
description: Various morphological measurements of wild caught band-winged
 grasshoppers. Please see relevant paper for full methodology.
description: Includes outlier individuals.
DOI: 10.5281/zenodo.16795313
title: GeoLocator Data Package: Scops Owl (MIGRALIGHT)

description: This datapackage contains geolocator data for scops owls (Otus scops) as part of the MIGRALIGHT project, funded by the Swiss Ornithological Institute and a Global Marie Skłodowska-Curie Actions (MSCA) Fellowship (HORIZON-MSCA-2023-PF-01-101150591).
DOI: 10.5281/zenodo.18396912
title: GeoLocator Data Package: Scops Owl (MIGRALIGHT)

description: This datapackage contains geolocator data for scops owls (Otus scops) as part of the MIGRALIGHT project, funded by the Swiss Ornithological Institute and a Global Marie Skłodowska-Curie Actions (MSCA) Fellowship (HORIZON-MSCA-2023-PF-01-101150591).
DOI: 10.5061/dryad.4qrfj6q99
title: Data for: Soil moisture, N, P, and forest cover effects on N fixation in alders in the southern boreal forest

description: Outside of tropical and arid regions, plant productivity is limited by the
 availability of soil N. Ironically, these are the regions where N-fixing
 plants are restricted to early successional habitats. The energy cost of N
 fixation has been used to explain the paucity of N-fixing plants in late
 successional ecosystems, and models predict reduced light and increased
 soil N availability will reduce N-fixing plant success. The lack of
 success of N-fixing plants has also been explained by their greater need
 for some elements, especially phosphorus. We examined the effect of N and
 P fertilizer over four years on N fixation in Alnus
 alnobetula spp. crispa in a
 mature Pinus banksiana forest in the southern boreal
 forest, and an adjacent site where wildfire had removed the tree canopy.
 We also monitored N fixation throughout two growing seasons examined the
 effect of artificial shading on photosynthesis. The addition of N or P
 fertilizer resulted in a 60% decrease in plant nodule nitrogenase
 activity. N fertilizer also reduced the proportion of cells in the root
 nodules containing N-fixing vesicles in the forest site. Shrubs in the
 forest had the highest photosynthetic rate when measured on a leaf mass
 basis,indicating an increased carbon capture efficiency compared to shrubs
 in the open. Over the course of two growing seasons, soil temperature had
 a positive effect on specific nitrogenase activity, and soil in the open
 site was warmer than soil in the forest in the spring. However, as soil
 moisture decreased, temperature was a weaker predictor of nitrogenase
 activity. Although all shrubs consistently acquired most of their N from
 fixation, shrubs in the forest derived more than shrubs in the open, which
 were more water limited. Overall, these results show that N- fixing plants
 may benefit from being in the understory for improved water balance in
 this region of the boreal forest. As such, light availability may not be
 the primary factor limiting the and abundance of N- fixing
 shrubs.
DOI: 10.5061/dryad.2ngf1vhnb
title: Delayed color maturation of a sexual ornament in males of a damselfly: crypsis, female mimicry or both?

description: Dynamic signals are a widespread phenomenon in several taxa, usually
 associated with intraspecific communication. On the other hand, dynamic
 iridescent signals are only detectable at specific angles of illumination;
 hence, the animal can hide the signal to avoid detection when necessary.
 This structural coloration is mostly dependent on illumination, contrast
 against the background and the vision of the receiver. Complex behavioural
 displays may be coupled with structural coloration to create dynamic
 visual signals that enhance these functions. Here, we addressed whether
 iridescence of males of a damselfly that inhabits dark rainforests,
 Chalcopteryx scintillans, can be considered a dynamic visual signal. We
 analyzed if coloration is perceived by conspecifics, while reducing
 detectability to eavesdroppers against three background types. Our results
 suggest that the visual background affects the detectability of male
 hindwings by different receivers, mostly predators and prey. We discuss if
 these results and the angle dependency of colour could be a mechanism to
 avoid unwanted intraspecific interactions or even to lure both predator
 and prey. We conclude that the dynamic iridescent signal functions are
 mostly to communicate with conspecifics while hindering the signal for
 prey, adding evidence of the multifunctionality of structural coloration
 coupled with behavioural displays in animals.
DOI: 10.5061/dryad.xwdbrv1d3
title: Evidence for hawkmoth pollination in the chiropterophilous African baobab (Adansonia digitata)

description: Chiropterophily, or bat pollination, is typically considered a highly
 specialized pollination system that has evolved independently numerous
 times across the angiosperm phylogeny, with distinct lineages often
 converging on a similar suite of floral traits. The African baobab,
 Adansonia digitata, occurs widespread across continental Africa and
 introduced throughout much of the tropics, possesses floral traits
 classically associated with bat pollination, namely nocturnal anthesis,
 pendulous white flowers, and a “musky” fragrance. Despite this, our
 observations and pollination exclusion experiments in South African baobab
 populations suggested little if any role for bats, but instead showed that
 hawkmoths are the main pollinators. Hand pollination indicated strong
 self-incompatibility and crossing experiments suggest minimal diurnal
 receptivity. Furthermore, our analyses of floral volatiles revealed not
 only sulfur-containing compounds, commonly associated with bat
 pollination, but also a high concentration of the sesquiterpene
 β-caryophyllene, a compound generally more typical of hawkmoth
 pollination. Comparing previous pollination studies and published floral
 scent profiles from West Africa suggests that the classic bat pollination
 system in baobabs may be more labile than previously thought. This study
 provides an empirical example of a species that most likely evolved due to
 bat pollination yet has some degree of generality and possible geographic
 variation in floral traits and pollinator visitation patterns across its
 range.
description: This dataset includes the Gas chromatography–mass spectrometry
 (GC-MS) data files, standard curves for emsission calcuations, and
 pollinator observation and treatment data.
DOI: 10.5061/dryad.x3ffbg7jj
title: The relationship between sternum variation and mode of locomotion in birds

description: Background: The origin of powered avian flight was a locomotor innovation
 that expanded the ecological potential of maniraptoran dinosaurs, leading
 to remarkable variation in modern birds (Neornithes). The avian sternum is
 the anchor for the major flight muscles and, despite varying widely in
 morphology, has not been extensively studied from evolutionary or
 functional perspectives. We quantify sternal variation across a broad
 phylogenetic scope of birds using 3D geometric morphometrics methods.
 Using this comprehensive dataset, we apply phylogenetically informed
 regression approaches to test hypotheses of sternum size allometry and the
 correlation of sternal shape with both size and locomotory capabilities,
 including flightlessness and the highly varying flight and swimming styles
 of Neornithes. Results: We find evidence for isometry of sternal size
 relative to body mass and document significant allometry of sternal shape
 alongside important correlations with locomotory capability, reflecting
 the effects of both body shape and musculoskeletal variation. Among these,
 we show that a large sternum with a deep or cranially projected sternal
 keel is necessary for powered flight in modern birds, that deeper sternal
 keels are correlated with slower but stronger flight, robust caudal
 sternal borders are associated with faster flapping styles, and that
 narrower sterna are associated with running abilities. Correlations
 between shape and locomotion are significant but show weak explanatory
 power, indicating that although sternal shape is broadly associated with
 locomotory ecology, other unexplored factors are also important.
 Conclusions: These results display the ecological importance of the avian
 sternum for flight and locomotion by providing a novel understanding of
 sternum form and function in Neornithes. Our study lays the groundwork for
 estimating the locomotory abilities of paravian dinosaurs, the ancestors
 to Neornithes, by highlighting the importance of this critical element for
 avian flight, and will be useful for future work on the origin of flight
 along the dinosaur-bird lineage.
DOI: 10.5061/dryad.prr4xgxkz
title: Responses of tropical tree seedlings in the forest-savanna boundary to combined effects of grass competition and fire

description: Co-occurring tree functional types (TFTs) within forest-savanna
 transitions may differ in seedling responses to grass competition and fire
 in savannas. We performed a common garden experiment in the Guinea savanna
 of Ghana to test hypotheses related to competition effects on growth,
 allocation to root storage reserves and subsequent survival responses to
 dry season fire for savanna-transitional TFT (i.e., species occurring both
 in forest and savanna) and forest TFT. The experiment included factorial
 combinations of TFT, comprising four species each of forest vs
 savanna-transitional trees, wet season grass competition vs no-grass
 competition, and dry season fire vs no-fire. Partly consistent
 with prediction, we found that grass competition suppressed tree seedling
 growth and caused a 17% reduction in root non-structural carbohydrates
 concentration [NSC] but had no effect on direct survival regardless of TFT
 at the end of the wet season. Post-fire survival averaged 6% for forest
 versus 91% for savanna-transitional TFTs across competition treatments. In
 contrast to our prediction that grass competition
 decreases post-fire seedling survival, wefound that a history of
 grass competition did not result in lower post-fire survival regardless of
 TFT, although plant mass, root mass fraction and root [NSC] at the end of
 the dry season were lower for tree seedlings with a history of
 competition. Our results demonstrate that grass competition suppresses
 tree seedling growth and root storage reserves irrespective of TFT, and
 that competition alone (without fire) may not preclude the establishment
 of forest seedlings in savannas close to forests.
description: Data were collected in a common garden experiment which spanned
 one complete wet season and one complete dry season in the Guinea savanna
 of Ghana, West Africa.
DOI: 10.15468/dl.95yfvy
title: Occurrence Download

description: A dataset containing 432180 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Country is one of (Canada, Mexico, United States of America)",
 "EventDate is greater than or equal to 2025-12-02",
 "EventDate is less than or equal to 2026-01-01",
 {
 "not" : {
 "Issue" : [
 "is one of (Basis of record invalid, Coordinate reprojection failed, Coordinate reprojection suspicious, Coordinate precision invalid, Coordinate uncertainty meters invalid, Country mismatch, Country invalid, Geodetic datum invalid, Presumed swapped coordinate, Presumed negated longitude, Presumed negated latitude, Country coordinate mismatch)"
 ]
 }
 },
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 432180 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002848-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.