cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dh8cv
title: Data from: Leaf drop affects herbivory in oaks

description: Leaf phenology is important to herbivores, but the timing and extent of
 leaf drop has not played an important role in our understanding of
 herbivore interactions with deciduous plants. Using phylogenetic general
 least squares regression, we compared the phenology of leaves of 55 oak
 species in a common garden with the abundance of leaf miners on those
 trees. Mine abundance was highest on trees with an intermediate leaf
 retention index, i.e. trees that lost most, but not all, of their leaves
 for 2–3 months. The leaves of more evergreen species were more heavily
 sclerotized, and sclerotized leaves accumulated fewer mines in the summer.
 Leaves of more deciduous species also accumulated fewer mines in the
 summer, and this was consistent with the idea that trees reduce
 overwintering herbivores by shedding leaves. Trees with a later leaf set
 and slower leaf maturation accumulated fewer herbivores. We propose that
 both leaf drop and early leaf phenology strongly affect herbivore
 abundance and select for differences in plant defense. Leaf drop may allow
 trees to dispose of their herbivores so that the herbivores must
 recolonize in spring, but trees with the longest leaf retention also have
 the greatest direct defenses against herbivores.
description: oak defenses leaf miners
 phenologyspecies-level data of
 phenology, herbivore associations, and defenses for 55 oak species in a
 common garden in Californiaoak data for
 dryad.csv
DOI: 10.5061/dryad.4cg3j
title: Data from: Genetic and environmental determinants of unreduced gamete production in Brassica napus, Sinapis arvensis and their hybrids

description: Unreduced gametes, sperm or egg cells with the somatic chromosome number,
 are an important mechanism of polyploid formation and gene flow between
 heteroploid plants. The meiotic processes leading to unreduced gamete
 formation are well documented, but the relative influence of environmental
 and genetic factors on the frequency of unreduced gametes remain largely
 untested. Furthermore, direct estimates of unreduced gametes based on DNA
 content are technically challenging and hence, uncommon. Here, we use flow
 cytometry to measure the contribution of genetic (hybridization) and
 environmental (nutrient limitation, wounding) changes to unreduced male
 gamete production in Brassica napus, Sinapis arvensis, and two hybrid
 lines. Treatments were applied to greenhouse grown plants in a random
 factorial design, with pollen sampled at two time intervals. Overall the
 frequency of unreduced gametes averaged 0.59% (range 0.06%-2.17%), plus a
 single outlier with 27%. Backcrossed hybrids had 39% to 75% higher
 unreduced gamete production than parental genotypes, averaged across all
 treatments, although the statistical significance of these differences
 depended on sampling period and wounding treatment. Unreduced gamete
 frequencies were higher for the second sampling period than the first.
 There were no direct effects of wounding or nutrient regime. Our results
 indicate that both genetic and environmental factors can induce increased
 unreduced gametes, highlighting the potential importance of environmental
 heterogeneity and genetic composition of populations in driving polyploid
 evolution
description: Sora.Kron.Husband_Factors.influcing.unreduced.gametesCSV data file of all plants used in analysis. Codes are included in data file
DOI: 10.5061/dryad.8j013
title: Data from: Beta-diversity on deep-sea wood falls reflects gradients in energy availability

description: Wood falls on the deep-sea floor represent a significant source of energy
 into the food-limited deep sea. Unique communities of primarily wood- and
 sulfide-obligate species form on these wood falls. However, little is
 known regarding patterns and drivers of variation in the composition of
 wood fall communities through space and time, and thus, how wood falls
 contribute to deep-sea biodiversity. Eighteen Acacia logs varying in size
 were placed and retrieved after five years at a 3200 m site in the Pacific
 Ocean. We found that the taxonomic composition and structure of deep-sea
 wood fall communities varied considerably and equated with considerable
 differences in energy usage and availability. Our findings suggest that
 natural variability in wood falls may contribute significantly to deep-sea
 diversity.
description: Wood Fall Data and
 Species Listwoodfall_species.csvR Script for Wood Fall Analyseswood_fall_beta_div.R
DOI: 10.5061/dryad.p9d27nh
title: Data from: Bottom-up trait-mediated indirect effects decrease pathogen transmission in a tritrophic system

description: A plant's induction of secondary defenses helps to decrease herbivore
 damage by changing resource quality. While these chemical or physical
 defenses may directly decrease herbivory, they can also have indirect
 consequences. In a tritrophic system consisting of a plant, an insect
 herbivore, and an insect pathogen, plant based trait-mediated indirect
 effects (TMIEs) can alter host-pathogen interactions and, thereby,
 indirectly affect disease transmission. In a series of field experiments,
 individual soybean plants (Glycine max) were sprayed with either a
 Jasmonic Acid (JA) solution to trigger induction of plant defenses or a
 similar control compound. Fall armyworm (Spodoptera frugiperda) larvae
 along with varying amounts of a lethal baculovirus were placed on the
 plants to measure transmission. Induction of plant defenses decreased
 viral transmission due to increased population heterogeneity arising from
 changes in individual susceptibility. The change in susceptibility via
 TMIEs was driven by a decrease in feeding rates and an increase viral dose
 needed to infect larvae. While the induction against herbivore attack may
 decrease herbivory, it can also decrease the efficacy of the
 herbivore's pathogen potentially to the plant's detriment. While
 TMIEs have been well-recognized for being driven by top-down forces,
 bottom-up interactions can dictate community dynamics and, here, epizootic
 severity.
description: Bottom-up trait-mediated
 indirect effects decrease pathogen transmission in a tritrophic
 systemZip file consisting of
 three comma delimited (csv) files that contain: 1) host-pathogen
 transmission data; 2) dose-response data; and, 3) preference data. The
 first row of the file contains the column headings associated with the
 data.Elderd-BottomupPathogenTransmission.zip
DOI: 10.5281/zenodo.18385405
title: Landscape-aware Automated Algorithm Design: An Efficient Framework for Real-world Optimization
DOI: 10.6084/m9.figshare.31157008
title: supplementary table1-9

description: We recruited 141 breastfed mother–child pairs from four Chinese cities, conducted a 6-year follow-up study, collected nutrition- and health-related data, and performed a combined analysis of children’s fecal and blood samples, as well as maternal breast milk and fecal samples.
DOI: 10.6084/m9.figshare.31157008.v1
title: supplementary table1-9

description: We recruited 141 breastfed mother–child pairs from four Chinese cities, conducted a 6-year follow-up study, collected nutrition- and health-related data, and performed a combined analysis of children’s fecal and blood samples, as well as maternal breast milk and fecal samples.
DOI: 10.5281/zenodo.18385404
title: Landscape-aware Automated Algorithm Design: An Efficient Framework for Real-world Optimization
DOI: 10.5061/dryad.g3mh0
title: Data from: The diet of an endemic subspecies of the Eurasian Spoonbill Platalea leucorodia balsaci, breeding at the Banc d’Arguin, Mauritania

description: In the period 1998–2010 the endemic subspecies of the Eurasian Spoonbill
 Platalea leucorodia balsaci breeding in Mauritania has decreased in
 numbers considerably. The causes for this decline are unknown. This study
 aimed to investigate the diet of the species. We analysed faecal material
 collected in the breeding colonies in 8 different years. The results show
 that Mauritanian Spoonbills almost exclusively eat shrimp (59.7%) and
 small fish (35.4%), the latter being dominated by Gobiidae (20.8%),
 Soleidae (4.8%) and Mugilidae (2.8%). Another 10 fish families were
 represented in small proportions. Shrimp were quantified on the basis of
 (parts of) mandibles present in the samples. All prey items eaten by the
 Spoonbills were extremely small. Diet composition of adult birds and
 chicks appeared to be similar. There was great variation in diet
 composition of adults between years, but there was no trend in any of the
 major diet components over the study period. This indicates that the
 decline of the Spoonbill population is not correlated with changes in food
 composition. Our diet study has been of a qualitative nature. Considering
 the dramatic population decline we plea for a more detailed ecological
 study of the species, including a quantitative approach of food intake and
 foraging conditions.
description: 1Spoonbill_adult_chick_dietFile containing diet composition of Spoonbill adults and chicks extracted from faecal material.2Spoonbill_diet_multiple_yearsDiet composition of Spoonbills extracted from faecal material collected in the period 1998-2010.
DOI: 10.5061/dryad.vn36290
title: Data from: Bat overpasses: an insufficient solution to restore habitat connectivity across roads

description: 1. Roads have many negative effects on wildlife, including their role in
 habitat fragmentation. Habitat fragmentation affects bats during their
 daily movements between roosts and foraging areas. As bats are protected
 in Europe, developers must implement specific mitigation measures that are
 hierarchically structured to achieve a null net impact. However, very few
 specific mitigation measures have been undertaken specifically for bats.
 Bat overpasses are among proposed improvements intended to reduce the
 impact of roads, but they have rarely been tested. The effectiveness of
 overpasses in facilitating safe road crossing of bats is critical for
 justifying the implementation of this mitigation measure. We therefore
 assessed whether bat overpasses are effectively used by bats. 2. We
 studied three bat overpasses with different designs in France. We
 developed an innovative method to characterize bat crossings using
 acoustic flight path reconstruction (AFPR). We used six pairs of stereo
 acoustic recorders in different habitat types that were located on both
 sides of the road, and operated simultaneously throughout the night. 3.
 Recording data contained 57 941 bat passes and 284 bat crossings from six
 species of bats at the three study sites. Our results suggest that
 crossings are more numerous if an overpass is located where bat commuting
 routes have been identified by environmental impact assessment. However,
 we found that the proportion of bat crossings along the commuting route
 was the same with or without an overpass; thus highlighting that bat
 overpasses do not fully restore habitat connectivity. 4. Synthesis and
 applications. Our study demonstrates that acoustic flight path
 reconstruction (AFPR) is a useful approach to obtain information on bat
 flight behaviour. We also emphasize the importance of field testing the
 effectiveness of mitigation measures, such as those intended to offset the
 impact of roads on biodiversity, and highlight that such measures should
 not be implemented based on their theoretical effectiveness alone.
description: Claireau_et_al_bat_crossingsNumber of bat crossings per site, per pair and per date within the context of the habitat (A, agricultural land; F, forest; H, hedgerow; O, bat overpass and S, stream).claireau_bat_crossings.txt
DOI: 10.5061/dryad.3st6vs3
title: Data from: The competition-dispersal trade-off exists in forbs but not in graminoids: a case study from multispecies alpine grassland communities

description: Much theoretical evidence has demonstrated that a trade-off between
 competitive and dispersal ability plays an important role in facilitating
 species coexistence. However, experimental evidence from natural
 communities is still rare. Here, we tested the competition-dispersal
 trade-off hypothesis in an alpine grassland in the Tianshan Mountains,
 Xinjiang, China, by quantifying competitive and dispersal ability using a
 combination of 4 plant traits (seed mass, ramet mass, height, and
 dispersal mode). Our results show that the competition-dispersal trade-off
 exists in the alpine grassland community and that this pattern was
 primarily demonstrated by forbs. The results suggest that most forb
 species are constrained to be either good competitors or good dispersers
 but not both, while there was no significant trade-off between competitive
 and dispersal ability for most graminoids. This might occur because
 graminoids undergo clonal reproduction, which allows them to find more
 benign microenvironments, forage for nutrients across a large area and
 store resources in clonal structures, and they are thus not strictly
 limited by the particular resources at our study site. To the best of our
 knowledge, this is the first time the CD trade-off has been tested for
 plants across the whole life cycle in a natural multispecies plant
 community, and more comprehensive studies are still needed to explore the
 underlying mechanisms and the linkage between the CD trade-off and
 community composition.
description: The raw data of
 ECE-2018-04-00490.R1The name list, plant
 traits (ramet mass (g), height (cm), seed mass (g), dispersal mode)
 competitive ability ranks and dispersal ability ranks of the species in
 our study site.appendix
 _data.csv
DOI: 10.5061/dryad.t130r
title: Data from: Genetic divergence between two phenotypically distinct bottlenose dolphin ecotypes suggests separate evolutionary trajectories

description: Due to their worldwide distribution and occupancy of different types of
 environments, bottlenose dolphins display considerable morphological
 variation. Despite limited understanding about the taxonomic identity of
 such forms and connectivity among them at global scale, coastal (or
 inshore) and offshore (or oceanic) ecotypes have been widely recognized in
 several ocean regions. In the Southwest Atlantic Ocean (SWA), however,
 there are scarce records of bottlenose dolphins differing in external
 morphology according to habitat preferences that resemble the
 coastal-offshore pattern observed elsewhere. The main aim of this study
 was to analyze the genetic variability, and test for population structure
 between coastal (n = 127) and offshore (n = 45) bottlenose dolphins
 sampled in the SWA to assess whether their external morphological
 distinction is consistent with genetic differentiation. We used a
 combination of mtDNA control region sequences and microsatellite genotypes
 to infer population structure and levels of genetic diversity. Our results
 from both molecular marker types were congruent and revealed strong levels
 of structuring (microsatellites FST = 0.385, p &lt; .001; mtDNA FST =
 0.183, p &lt; .001; ΦST = 0.385, p &lt; .001) and much lower
 genetic diversity in the coastal than the offshore ecotype, supporting
 patterns found in previous studies elsewhere. Despite the opportunity for
 gene flow in potential “contact zones”, we found minimal current and
 historical connectivity between ecotypes, suggesting they are following
 discrete evolutionary trajectories. Based on our molecular findings, which
 seem to be consistent with morphological differentiations recently
 described for bottlenose dolphins in our study area, we recommend
 recognizing the offshore bottlenose dolphin ecotype as an additional
 Evolutionarily Significant Unit (ESU) in the SWA. Implications of these
 results for the conservation of bottlenose dolphins in SWA are also
 discussed.
description: Genetic data Tursiops
 Southwest Atlantic33 identified sequences
 from the analysis of 458bp of D-loop control region (mtDNA) and genotyping
 data from 11 microsateliltes used to investigate pop. structure and
 diversity in bottlenose dolphins sampled along the Southwest Atlantic
 Ocean.Fruet_et_al_2017_genetic_data.TXT.zip
DOI: 10.5061/dryad.2t99d
title: Data from: Asexual queen succession in the higher termite Embiratermes neotenicus

description: Asexual queen succession (AQS), in which workers, soldiers and dispersing
 reproductives are produced sexually while numerous non-dispersing queens
 arise through thelytokous parthenogenesis, has recently been described in
 three species of lower termites of the genus Reticulitermes. Here, we show
 that AQS is not an oddity restricted to a single genus of lower termites,
 but a more widespread strategy occurring also in the most advanced termite
 group, the higher termites (Termitidae). We analysed the genetic structure
 in 10 colonies of the Neotropical higher termite Embiratermes neotenicus
 (Syntermitinae) using five newly developed polymorphic microsatellite
 loci. The colonies contained one primary king accompanied either by a
 single primary queen or by up to almost 200 neotenic queens. While the
 workers, the soldiers and most future dispersing reproductives were
 produced sexually, the non-dispersing neotenic queens originated through
 thelytokous parthenogenesis of the founding primary queen. Surprisingly,
 the mode of thelytoky observed in E. neotenicus is most probably automixis
 with central fusion, contrasting with the automixis with terminal fusion
 documented in Reticulitermes. The occurrence of AQS based on different
 mechanisms of ploidy restoration raises the hypothesis of an independent
 evolutionary origin of this unique reproductive strategy in individual
 lineages of lower and higher termites.
description: Embiratermes neotenicus
 COI haplotypesCytochrome oxidase I
 (COI) unique haplotypes for Embiratermes neotenicus samples. Sequence ID,
 country, specimen voucher and GenBank accession number are
 indicated.EneotenicusCOI.fas
DOI: 10.5061/dryad.2c5m1
title: Data from: Micropyle number is associated with elevated female promiscuity in Lepidoptera

description: In the majority of insects, sperm fertilize the egg via a narrow canal
 through the outer chorion called the micropyle. Despite having this one
 primary function, there is considerable unexplained variation in the
 location, arrangement and number of micropyles within and between species.
 Here, we examined the relationship between micropyle number and female
 mating pattern through a comparative analysis across Lepidoptera. Three
 functional hypotheses could explain profound micropylar variation: (i)
 increasing micropyle number reduces the risk of infertility through sperm
 limitation in species that mate infrequently; (ii) decreasing micropyle
 number reduces the risk of pathological polyspermy in species that mate
 more frequently; and (iii) increasing micropyle number allows females to
 exert greater control over fertilization within the context of
 post-copulatory sexual selection, which will be more intense in
 promiscuous species. Micropyle number was positively related to the degree
 of female promiscuity as measured by spermatophore count, regardless of
 phylogenetic signal, supporting the hypothesis that micropyle number is
 shaped by post-copulatory sexual selection. We discuss this finding in the
 context of cryptic female choice, sperm limitation and physiological
 polyspermy.
description: Micropyle number and
 spermatophore count dataData used to calculate
 the relationship between micropyle number and spermatophore count in
 Lepidoptera.Iossa_et_al_2016_Biol_Let.csv
DOI: 10.5061/dryad.6pq3250
title: Data from: The unfolding of plant growth form-defence syndromes along elevation gradients

description: Understanding the functional economics that drives plant investment of
 resources requires investigating the interface between plant phenotypes
 and the variation in ecological conditions. While allocation to defence
 represents a large portion of the carbon budget, this axis is usually
 neglected in the study of plant economic spectrum. Using a novel
 geometrical approach, we analysed the co‐variation in a comprehensive set
 of functional traits related to plant growth strategies, as well as
 chemical defences against herbivores on all 15 Cardamine species present
 in the Swiss Alps. By extracting geometrical information of the functional
 space, we observed clustering of plants into three main syndromes. Those
 different strategies of growth form and defence were also distributed
 within distinct elevational bands demonstrating an association between the
 functional space and the ecological conditions. We conclude that plant
 strategies converge into clear syndromes that trade off abiotic tolerance,
 growth and defence within each elevation zone.
description: all traits
 averagesspecies-level averages
 for 15 species of cardamine growing in the Alps.
DOI: 10.5281/zenodo.17984470
title: SHM_415340_HST_3D

description: Photogrammetric 3D model of an Early Neolithic polygonal axe collected from Skåne and held in the collections of the National Historical Museums in Stockholm.

Link to the Dynamic Collection platform  

https://dyncolldev.ht.lu.se/plus/artifact_view.php?item=694

Link to Sök I Samlingarna  

https://samlingar.shm.se/object/9093CDFD-7ED0-4AC4-9F54-44670BBCD57D
DOI: 10.5281/zenodo.17984471
title: SHM_415340_HST_3D

description: Photogrammetric 3D model of an Early Neolithic polygonal axe collected from Skåne and held in the collections of the National Historical Museums in Stockholm.

Link to the Dynamic Collection platform  

https://dyncolldev.ht.lu.se/plus/artifact_view.php?item=694

Link to Sök I Samlingarna  

https://samlingar.shm.se/object/9093CDFD-7ED0-4AC4-9F54-44670BBCD57D
DOI: 10.5061/dryad.003k4g0
title: Data from: Priority effects within coinfected hosts can drive unexpected population-scale patterns of parasite prevalence

description: Organisms are frequently coinfected by multiple parasite strains and
 species, and interactions between parasites within hosts are known to
 influence parasite prevalence and diversity, as well as epidemic timing.
 Importantly, interactions between coinfecting parasites can be affected by
 the order in which they infect hosts (i.e. within-host priority effects).
 In this study, we use a single-host, two-pathogen, SI model with
 environmental transmission to explore how within-host priority effects
 scale up to alter host population-scale infection patterns. Specifically,
 we ask how parasite prevalence changes in the presence of different types
 of priority effects. We consider two scenarios without priority effects
 and four scenarios with priority effects where there is either an
 advantage or a disadvantage to being the first to infect in a coinfected
 host. Models without priority effects always predict negative
 relationships between the prevalences of both parasites. In contrast,
 models with priority effects can yield unimodal prevalence relationships
 where the prevalence of a focal parasite is minimized or maximized at
 intermediate prevalences of a coinfecting parasite. The mechanism behind
 this pattern is that as the prevalence of the coinfecting parasite
 increases, most infections of the focal parasite change from occurring as
 solo infections, to first arrival coinfections, to second arrival
 coinfections. The corresponding changes in parasite fitness as the focal
 parasite moves from one infection class to another then map to changes in
 focal parasite prevalence. Further, we found that even when parasites
 interact negatively within a host, they still can have positive prevalence
 relationships at the population scale. These results suggest that
 within-host priority effects can change host population-scale infection
 patterns in systematic (and initially counterintuitive) ways, and that
 taking them into account may improve disease forecasting in coinfected
 populations.
description: Priority_Effects_Model_OikosThis script runs the model described in equations 1-7, and which creates the data behind figures 2-5.