cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.hj8fr
title: Data from: Seasonal cycles, phylogenetic assembly, and functional diversity of orchid bee communities

description: Neotropical rainforests sustain some of the most diverse terrestrial
 communities on Earth. Euglossine (or orchid) bees are a diverse lineage of
 insect pollinators distributed throughout the American tropics, where they
 provide pollination services to a staggering diversity of flowering plant
 taxa. Elucidating the seasonal patterns of phylogenetic assembly and
 functional trait diversity of bee communities can shed new light into the
 mechanisms that govern the assembly of bee pollinator communities and the
 potential effects of declining bee populations. Male euglossine bees
 collect, store, and accumulate odoriferous compounds (perfumes) to
 subsequently use during courtship display. Thus, synthetic chemical baits
 can be used to attract and monitor euglossine bee populations. We
 conducted monthly censuses of orchid bees in three sites in the Magdalena
 valley of Colombia – a region where Central and South American biotas
 converge – to investigate the structure, diversity, and assembly of
 euglossine bee communities through time in relation to seasonal climatic
 cycles. In particular, we tested the hypothesis that phylogenetic
 community structure and functional trait diversity changed in response to
 seasonal rainfall fluctuations. All communities exhibited strong to
 moderate phylogenetic clustering throughout the year, with few pronounced
 bursts of phylogenetic overdispersion that coincided with the transition
 from wet-to-dry seasons. Despite the heterogeneous distribution of
 functional traits (e.g., body size, body mass, and proboscis length) and
 the observed seasonal fluctuations in phylogenetic diversity, we found
 that functional trait diversity, evenness, and divergence remained
 constant during all seasons in all communities. However, similar to the
 pattern observed with phylogenetic diversity, functional trait richness
 fluctuated markedly with rainfall in all sites. These results emphasize
 the importance of considering seasonal fluctuations in community assembly
 and provide a glimpse to the potential effects that climatic alterations
 may have on both pollinator communities and the ecosystem services they
 provide.
description: DNA
 MatrixDNA matrix used to
 generate phylogenetic treeseg6.nex
DOI: 10.5061/dryad.16df2
title: Data from: Ontogenetic adaptations in the visual systems of deep-sea crustaceans

description: For all visually competent organisms, the driving force behind the
 adaptation of photoreceptors involves obtaining the best balance of
 resolution to sensitivity in the prevailing light regime, as an increase
 in sensitivity often results in a decrease in resolution. A number of
 marine species have an additional problem to deal with, in that the
 juvenile stages live in relatively brightly lit shallow (100–200 m depth)
 waters, whereas the adult stages have daytime depths of more than 600 m,
 where little downwelling light remains. Here, I present the results of
 electrophysiological analyses of the temporal resolution and irradiance
 sensitivity of juvenile and adult stages of two species of ontogenetically
 migrating crustaceans (Gnathophausia ingens and Systellaspis debilis) that
 must deal with dramatically different light environments and temperatures
 during their life histories. The results demonstrate that there are
 significant effects of temperature on temporal resolution, which help to
 optimize the visual systems of the two life-history stages for their
 respective light environments.
description: Sys deb FF adulvs vs.
 juvenilesComposit flicker fusion
 data for adult and juvenile specimens of Systellaspis
 debilisSys
 deb ff adults vs. juvies.xlsV log I adults vs
 juveniles sys debVoltage vs. log
 intensity for adults and juveniles specimens of Systellaspis
 debilisgnatho latency data 5 7
 10Response latency data
 for Gnathophausia ingens adults and juveniles at 3 different
 temperaturesGnatho Vlog I juvie vs.
 adultVoltage vs. log
 intensity data for juvenile and adult specimens of Gnathophausia
 ingensflicker fusion
 Gnathophausia ingensFlicker fusion data for
 Gnathophausia ingens adults and juvenilesG. ingens
 FF.xls
DOI: 10.5061/dryad.78568
title: Data from: The consequences of polyandry for sibship structures, distributions of relationships and relatedness, and potential for inbreeding in a wild population

description: The evolutionary benefits of simultaneous polyandry (female multiple
 mating within a single reproductive event) remain elusive. One potential
 benefit could arise if polyandry alters sibship structures and consequent
 relationships and relatedness among females' descendants, and thereby
 intrinsically reduces future inbreeding risk (the 'indirect
 inbreeding avoidance hypothesis'). However such effects have not been
 quantified in naturally complex mating systems that also encompass
 iteroparity, overlapping generations, sequential polyandry, and polygyny.
 We used long-term social and genetic pedigree data from song sparrows
 (Melospiza melodia) to quantify cross-generational consequences of
 simultaneous polyandry for offspring sibship structures and distributions
 of relationships and relatedness among possible mates. Simultaneous
 polyandry decreased full-sibships and increased half-sibships on average,
 but such effects varied among females and were smaller than would occur in
 the absence of sequential polyandry or polygyny. Further, while
 simultaneous polyandry decreased the overall frequencies of possible
 matings among adult full-sibs, it increased the frequencies of possible
 matings among adult half-sibs and more distant relatives. These results
 imply that the intrinsic consequences of simultaneous polyandry for
 inbreeding risk could cause weak indirect selection on polyandry, but the
 magnitude and direction of such effects will depend on complex
 interactions with other mating system components and the form of
 inbreeding depression.
description: Sibship_Structures_Females_BANDED_offspringThis file includes the sibship structures among all females' banded offspring, given the social pedigree, genetic pedigree, and 'distinct males assumption'.Sibship_Structures_Females_RECRUITED_offspringThis file includes the sibship structures among all females' recruited offspring, given the social pedigree, genetic pedigree, and 'distinct males assumption'.Sibship_Structures_Males_BANDED_offspringThis file includes the sibship structures among all males' banded offspring, given the social and genetic pedigrees.Sibship_Structures_Males_RECRUITED_offspringThis file includes the sibship structures among all males' recruited offspring, given the social and genetic pedigrees.Relationships_and_Relatedness_All_Possible_Female_Male_PairsThis file contains all possible female-male pairings from 2008-2015, as well as the relationship and relatedness among each pair, as calculated from both a social (ie no polyandry) and genetic (ie including polyandry) pedigree.
DOI: 10.5061/dryad.8m10n2mq
title: Data from: Evolutionary consequences of microhabitat: population-genetic structuring in kelp- versus rock-associated chitons

description: Rafting has long been invoked as a key marine dispersal mechanism, but
 biologists have thus far produced little genetic evidence to support this
 hypothesis. We hypothesise that coastal species associated with buoyant
 seaweeds should experience enhanced population connectivity due to
 rafting. In particular, invertebrates strongly associated with the buoyant
 bull-kelp Durvillaea antarctica might be expected to have lower levels of
 population genetic differentiation than taxa mainly exploiting non-buoyant
 substrates. We undertook a comparative genetic study of two
 co-distributed, congeneric chiton species, assessing population
 connectivity at scales of 61-516 km, using ≥186 polymorphic AFLP loci per
 species. Consistent with predictions, population genetic differentiation
 was weaker in the kelp-associated Sypharochiton sinclairi than in the
 rock-associated S. pelliserpentis. Additionally, while we found a
 significant positive correlation between genetic and oceanographic
 distances in both chiton species, the correlation was stronger in S.
 pelliserpentis (R2 = 0.28) than in S. sinclairi (R2 = 0.18). These data
 support the hypothesis that epifaunal taxa can experience enhanced
 population-genetic connectivity as a result of their rafting-ability.
description: DataSheet1_14795630MEC-11-0819DataSheet2_14795630MEC-11-0819DataSheet3_14795630MEC-11-0819
DOI: 10.5281/zenodo.13318707
title: Menschen afrikanischer, asiatischer sowie indigen- und afrikanisch-amerikanischer Herkunft im Hamburger Raum, 1760 bis 1840

description: Dieser prosopographische Datensatz ist aus der Recherche zu einem Dissertationsprojekt der Autorin zu Hamburger Sklavereiverbindungen und nicht-weißen Menschen im Hamburger Raum hervorgegangen, die von 2017 bis 2024 an der Universität Bremen durchgeführt wurde. Es erfasst Personen afrikanischer, asiatischer sowie indigen- oder afrikanisch-amerikanischer Herkunft, die sich zwischen 1760 und 1840 im Hamburger Raum aufhielten und sich durch Sekundärliteratur oder Quellen nachweisen lassen. Die Datenbank stellt ein Teilergebnis der Forschung dar, die in der zugehörigen Dissertation ausgewertet, kontextualisiert und analysiert wird. In die Datenbank aufgenommen wurden Individuen oder – so sich keine Einzelangaben ausfindig machen ließen – kleine Gruppen, die sich nachweislich über kürzere oder längere Zeiträume im heutigen Hamburger Stadtgebiet sowie in angrenzende Gemeinden wie Ahrensburg und Pinneberg aufhielten. Da die Datenbank ein Resultat einer gezielten Recherche ist, kann sie keinen Anspruch auf Vollständigkeit oder Repräsentativität (etwa in Bezug auf Herkunftsregionen) erheben. Ergänzende Informationen zum Quellenkorpus finden sich im Dokument „Durchgesehene serielle Quellen“; weitere Informationen zu den in der Datenbank genutzten Quellen sind im Dokument „Erläuterungen zu Spalten und Angabeoptionen“ einzusehen.
DOI: 10.5281/zenodo.18381462
title: Menschen afrikanischer, asiatischer sowie indigen- und afrikanisch-amerikanischer Herkunft im Hamburger Raum, 1760 bis 1840

description: Dieser prosopographische Datensatz ist aus der Recherche zu einem Dissertationsprojekt der Autorin zu Hamburger Sklavereiverbindungen und nicht-weißen Menschen im Hamburger Raum hervorgegangen, die von 2017 bis 2024 an der Universität Bremen durchgeführt wurde. Es erfasst Personen afrikanischer, asiatischer sowie indigen- oder afrikanisch-amerikanischer Herkunft, die sich zwischen 1760 und 1840 im Hamburger Raum aufhielten und sich durch Sekundärliteratur oder Quellen nachweisen lassen. Die Datenbank stellt ein Teilergebnis der Forschung dar, die in der zugehörigen Dissertation ausgewertet, kontextualisiert und analysiert wird. In die Datenbank aufgenommen wurden Individuen oder – so sich keine Einzelangaben ausfindig machen ließen – kleine Gruppen, die sich nachweislich über kürzere oder längere Zeiträume im heutigen Hamburger Stadtgebiet sowie in angrenzende Gemeinden wie Ahrensburg und Pinneberg aufhielten. Da die Datenbank ein Resultat einer gezielten Recherche ist, kann sie keinen Anspruch auf Vollständigkeit oder Repräsentativität (etwa in Bezug auf Herkunftsregionen) erheben. Ergänzende Informationen zum Quellenkorpus finden sich im Dokument „Durchgesehene serielle Quellen“; weitere Informationen zu den in der Datenbank genutzten Quellen sind im Dokument „Erläuterungen zu Spalten und Angabeoptionen“ einzusehen.
DOI: 10.5061/dryad.qv871g8
title: Data from: Metabolic physiology explains macroevolutionary trends in the melanic colour system across amniotes

description: Metabolism links organisms to their environment through its effects on
 thermoregulation, feeding behaviour, and energetics. Genes involved in
 metabolic processes have known pleiotropic effects on some melanic colour
 traits. Understanding links between physiology and melanic colour is
 critical for understanding the role of, and potential constraints on,
 colour production. Despite considerable variation in metabolic rates and
 presumed ancestral melanic colouration in vertebrates, few studies have
 looked at a potential relationship between these two systems in a
 comparative framework. Here, we test the hypothesis that changes in
 melanosome shape in integumentary structures track metabolic rate
 variation across amniotes. Using multivariate comparative analyses and
 incorporating both extant and fossil taxa, we find significantly faster
 rates of melanosome shape evolution in taxa with high metabolic rates, as
 well as both colour- and clade-specific differences in the relationship
 between metabolic rate and melanosome shape. Phylogenetic tests recover an
 expansion in melanosome morphospace in maniraptoran dinosaurs, as well as
 rate shifts within birds (in songbirds) and mammals. These findings
 indicate another core phenotype influenced by metabolic changes in
 vertebrates. They also provide a framework for testing clade-specific gene
 expression patterns in the melanocortin system, and may improve colour
 reconstructions in extinct taxa.
description: R function to add
 fossils to a treeaddfossiltree.RAmniotes tree (15423 taxa)bmr_amniotes_full15423.trePruned treebmr_pruned_all.trePruned tree (extant taxa only)bmr_pruned_extant.treTrait datasetbmr-final_dataset.csvR function to run ratebystate test with multivariate databmr-ratebystatemulti.R
DOI: 10.5061/dryad.6v75k
title: Data from: Selective logging in tropical forests decreases the robustness of liana-tree interaction networks to the loss of host tree species

description: Selective logging is one of the major drivers of tropical forest
 degradation, causing important shifts in species composition. Whether such
 changes modify interactions between species and the networks in which they
 are embedded remain fundamental questions to assess the ‘health’ and
 ecosystem functionality of logged forests. We focus on interactions
 between lianas and their tree hosts within primary and selectively logged
 forests in the biodiversity hotspot of Malaysian Borneo. We found that
 lianas were more abundant, had higher species richness and different
 species compositions in logged than in primary forests. Logged forests
 showed heavier liana loads disparately affecting slow-growth tree species,
 which could exacerbate the loss of timber value and carbon storage already
 associated to logging. Moreover, simulation scenarios of host tree local
 species loss indicated that logging might decrease the robustness of
 liana-tree interaction networks if heavily infested trees (i.e. the most
 connected ones) are more likely to disappear. This effect is partially
 mitigated in the short term by the colonization of host trees by a greater
 diversity of liana species within logged forests, yet this might not
 compensate for the loss of preferred tree hosts in the long term. As a
 consequence, species interaction networks may show a lagged response to
 disturbance, which may trigger sudden collapses in species richness and
 ecosystem function in response to additional disturbances, representing a
 new type of “extinction debt”.
description: borneo
 datasetIncludes liana and tree
 species, DBH and host used by lianas across 120 sample plots in primary
 and logged forest
DOI: 10.5061/dryad.60h3r
title: Data from: Effects of prior exposure to antibiotics on bacterial adaptation to phages

description: Understanding adaptation to complex environments requires information
 about how exposure to one selection pressure affects adaptation to others.
 For bacteria, antibiotics and viral parasites (phages) are two of the most
 common selection pressures and are both relevant for treatment of
 bacterial infections: increasing antibiotic resistance is generating
 significant interest in using phages in addition or as an alternative to
 antibiotics. However, we lack knowledge of how exposure to antibiotics
 affects bacterial responses to phages. Specifically, it is unclear how the
 negative effects of antibiotics on bacterial population growth combine
 with any possible mutagenic effects or physiological responses to
 influence adaptation to other stressors such as phages, and how this net
 effect varies with antibiotic concentration. Here, we experimentally
 addressed the effect of pre-exposure to a wide range of antibiotic
 concentrations on bacterial responses to phages. Across 10 antibiotics, we
 found a strong association between their effects on bacterial population
 size and subsequent population growth in the presence of phages (which in
 these conditions indicates phage-resistance evolution). We detected some
 evidence of mutagenesis among populations treated with fluoroquinolones,
 quinolones and β-lactams at sub-lethal doses, but these effects were small
 and not consistent across phage treatments. These results show that,
 although stressors such as antibiotics can boost adaptation to other
 stressors at low concentrations, these effects are weak compared to the
 effect of reduced population growth at inhibitory concentrations, which in
 our experiments strongly reduced the likelihood of subsequent
 phage-resistance evolution.
description: AB-Phage_experimentAntibiotic-Phage experiment datasetFluctuationTestFluctuation test datasetGradient_experimentGradient experiment
DOI: 10.5061/dryad.3sd60
title: Data from: Linking topological structure and dynamics in ecological networks

description: Interaction networks are basic descriptions of ecological communities and
 are at the core of community dynamics models. Knowledge of their structure
 should enable us to understand dynamical properties of ecological
 communities. However, the relationships between dynamical properties of
 communities and qualitative descriptors of network structure remain
 unclear. To improve our understanding of such relationships, we develop a
 framework based on the concept of strongly connected components, which are
 key structural components of networks necessary to explain stability
 properties such as persistence and robustness. We illustrate this
 framework for the analysis of qualitative empirical food webs and
 plant-plant interaction networks. Both types of networks exhibit high
 persistence (on average, 99% and 80% of species, respectively, are
 expected to persist) and robustness (only 0.2% and 2% of species are
 expected to disappear following the extinction of a species). Each of the
 networks is structured as a large group of interconnected species
 accompanied by much smaller groups that most often consist of a single
 species. This low-modularity configuration can be explained by a negative
 modularity-stability relationship. Our results suggest that ecological
 communities are not typically structured in multispecies compartments and
 that compartmentalization decreases robustness.
description: Replacement
 networksAdjacency matrices of 10
 plant-plant replacement networks.
DOI: 10.18738/t8/zloenv
title: Transport spin polarization in RuO2 films

description: Dataset supporting the manuscript "Transport spin polarization in RuO2 films"
DOI: 10.5061/dryad.58fp6
title: Data from: Phylogenetic relationships in Asarum (Aristolochiaceae): effect of data partitioning and a revised classification

description: Premise of the study: Generic boundaries and infrageneric relationships
 among the charismatic temperate magnoliid Asarum sensu lato have long been
 uncertain. Previous molecular phylogenetic analyses used either plastid or
 nuclear loci alone and varied greatly in their taxonomic implications for
 the genus. We analyze additional molecular markers from the nuclear and
 plastid genomes, reevaluate the possibility of a derived loss of
 autonomous self-pollination, and investigate the topological effects of
 matrix partitioning scheme choice. Methods: We sequenced seven plastid
 regions and the nuclear ITS1 - ITS2 region of 58 individuals representing
 all previously recognized Asarum s.l. segregate genera and the monotypic
 genus Saruma. Matrices were partitioned using common a priori partitioning
 schemes and PartitionFinder. Key results: Topologies recovered using a
 priori partitioning of matrices differed from those recovered using a
 PartitionFinder-selected scheme, and by analysis method. We recover six
 monophyletic groups that we circumscribe into three subgenera and six
 sections. Putative fungal mimic characters serve as synapomorphies only
 for subgenus Heterotropa. Subgenus Geotaenium, a new subgenus, is
 recovered as sister to the remainder of Asarum by ML analyses of highly
 partitioned datasets. Section Longistylis, also newly named, is sister to
 section Hexastylis. Conclusions: Our analyses do not unambiguously support
 a single origin for all fungal mimicry characters. Topologies recovered
 through the analysis of PartitionFinder-optimized matrices can differ
 drastically from those inferred from a priori partitioned matrices and by
 analytical method. We recommend that investigators evaluate the
 topological effects of matrix partitioning using multiple methods of
 phylogenetic reconstruction.
description: Combined (Plastid and
 Nuclear) MatrixSanger sequenced plastid
 and nuclear loci aligned using MAFFT through Geneious 5-7 (default
 alignment values).Concatenated Chloro and ITS
 Final BEST.nexusRAxML Matrix 6
 bipartitions treeMost likely tree
 resulting from RAxML analysis of Matrix 6, annotated with bootstrap
 values.RAxML_bipartitions.matrix6.treBEAST Tree from Matrix 6BI tree resulting from the analysis of Matrix 6 with BEAST.MATRIX6BeastTree.nex
DOI: 10.5061/dryad.b5151
title: Data from: Biased generalization of salient traits drives the evolution of warning signals

description: The importance of receiver biases in shaping the evolution of many
 signalling systems is widely acknowledged. Here we show that receiver bias
 can explain which traits evolve to become warning signals. For warning
 colouration, a generalization bias for a signalling trait can result from
 predators learning to discriminate unprofitable from profitable prey.
 However, since the colour patterns of prey are complex traits with
 multiple components, it is crucial to understand which of the many aspects
 of prey appearance evolve into signals. We provide experimental evidence
 that the more salient differences in prey traits give rise to greater
 generalization bias, corresponding to stronger selection towards trait
 exaggeration. Our results are based on experiments with domestic chickens
 as predators in a Skinner-box-like setting, and imply that the difference
 in appearance between profitable and unprofitable prey that is most
 rapidly learnt produces the greatest generalization bias. As a
 consequence, certain salient traits of unprofitable prey are selected
 towards exaggeration to even higher salience, driving the evolution of
 warning colouration. This general idea may also help to explain the
 evolution of many other striking signalling traits found in nature.
description: Data and R script
 filesFiles with data, R code,
 and documentation for the study: Biased generalization of salient traits
 drives the evolution of warning signals, by Gabriella Gamberale-Stille,
 Baharan Kazemi, Alexandra Balogh and Olof Leimar.DataDryad.zip