cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tb2rbp025
title: Data for: Risky business: Males choose more receptive adults over safer subadults in a cannibalistic spider

description: Understanding factors affecting male mate choice can be important for
 tracking the dynamics of sexual selection in nature. Contextual variation
 in reproductive costs and benefits of different types of mates may predict
 male choice, but mating may also be opportunistic regardless of female
 reproductive value. Male brown widow spiders (Latrodectus geometricus) can
 mate with adult as well as immature (subadult) females. Matings with
 adults require costly courtship and typically end with cannibalism
 (‘self-sacrifice’ initiated by a male somersault), but matings with
 subadults involve more brief courtship and no risk of cannibalism. We
 examined whether there was evidence for male mate choice as a function of
 risks associated with different types of mates and the cues available to
 courting males. Previous studies showed male preference for adult females
 based on airborne pheromones. In our study, males preferred adult females
 based on silk-borne contact cues. We swapped adult and subadult females
 between webs to determine which cues trigger different components of
 courtship, and showed that contact with adult females’ webs triggers web
 reduction and contact with adult females’ bodies triggers mate binding and
 somersaulting, but vibratory courtship occurs regardless of the origin of
 the web or female developmental stage. We conclude that males can detect
 and recognize subadult females as potential mating partners, but are more
 likely to invest in costly courtship behaviours and mating attempts with
 adults. In our experiments, subadult females were less likely to mate than
 adults. We conclude that mating with adults could be the preferred option
 for males because of the higher likelihood of copulation, even at the cost
 of a higher risk of cannibalism.
description: Data were collected in two laboratory experiments:
 1) Male responses to subadult vs. adult female silk cues in a
 Y-maze 2-choice experiment 2) Outcomes of mating trials
 in which males courted subadult or adult females placed on the webs of
 other females in a fully crossed design All analyses
 were conducted in R version 4.0.0. See paper for full details of
 experimental design and analysis.
DOI: 10.5061/dryad.6m905qg16
title: Data from: Collateral sensitivity interactions between antibiotics depend on local abiotic conditions

description: Mutations conferring resistance to one antibiotic can increase (cross
 resistance) or decrease (collateral sensitivity) resistance to others.
 Antibiotic combinations displaying collateral sensitivity could be used in
 treatments that slow resistance evolution. However, lab-to-clinic
 translation requires understanding whether collateral effects are robust
 across different environmental conditions. Here, we isolated and
 characterized resistant mutants of Escherichia coli using five
 antibiotics, before measuring collateral effects on resistance to other
 paired antibiotics. During both isolation and phenotyping, we varied
 conditions in ways relevant in nature (pH, temperature, bile). This
 revealed local abiotic conditions modified expression of resistance
 against both the antibiotic used during isolation and other antibiotics.
 Consequently, local conditions influenced collateral sensitivity in two
 ways: by favouring different sets of mutants (with different collateral
 sensitivities), and by modifying expression of collateral effects for
 individual mutants. These results place collateral sensitivity in the
 context of environmental variation, with important implications for
 translation to real-world applications.
description: Whole genome resequencing data of Escherichia coli selected with
 antibiotics, paired with assays of phenotypes related to
 resistance.
description: Readme file included.
DOI: 10.5061/dryad.q573n5tjz
title: Data from: Differences in sibling cooperation in presence and absence of parental care in a genus with interspecific variation in offspring dependence

description: The widely spread evolutionary strategy of parental care is considered an
 important driver of social evolution. While offspring were long thought to
 primarily interact competitively, recent studies revealed the potential
 importance of sibling cooperation. Theories suggest that the degree of
 cooperation in offspring interactions depends on the degree of offspring
 dependence on parental care: offspring unable to forage on their own
 should compete more, whereas more independent juveniles may increase the
 degree of cooperation. In this study, we tested the occurrence of sibling
 cooperation in the absence of post-hatching care in several burying beetle
 species exhibiting varying degrees of offspring dependence. To this end,
 we measured larval growth rate and survival in the presence and absence of
 pre-hatching care using different brood sizes. We found that sibling
 cooperation cannot be exclusively explained by offspring dependence on
 parental care. While only species with more independent larvae cooperated
 when receiving pre-hatching care, larval cooperation occurred across
 species in the absence of care. The latter result suggests that sibling
 cooperation was already present in an early ancestor of the genus
 Nicrophorus. Overall, these findings give important insights into the
 transition from facultative to obligate family life.
description: This excel file contains data from the laboratory described in
 the article. 
description: This is the data file associated with the cooperation experiment.
 Please check the first sheet in the file for further details regarding the
 individual columns. The second sheet contains the data for the
 experiment.
DOI: 10.5061/dryad.9s4mw6mht
title: Data from: Multidecadal changes in functional diversity lag behind the recovery of taxonomic diversity

description: 1. While there has been increasing interest in how taxonomic diversity is
 changing over time, less is known about how long-term taxonomic changes
 may affect ecosystem functioning and resilience. Exploring long-term
 patterns of functional diversity can provide key insights into the
 capacity of a community to carry out ecological processes and the
 redundancy of species’ roles. 2. We focus on a protected freshwater system
 located in a national park in southeast Germany. We use a high-resolution
 benthic macroinvertebrate dataset spanning 32 years (1983 – 2014) and test
 if changes in functional diversity are reflected in taxonomic diversity
 using a multidimensional trait-based approach and regression analyses.
 Specifically, we asked: i) How has functional diversity changed over time?
 ii) How functionally distinct are the community’s taxa? iii) Are changes
 in functional diversity concurrent with taxonomic diversity? iv) What is
 the extent of community functional redundancy? 3. Resultant from
 acidification mitigation, macroinvertebrate taxonomic diversity increased
 over the study period. Recovery of functional diversity was less
 pronounced, lagging behind responses of taxonomic diversity. Over
 multi-decadal timescales, the macroinvertebrate community has become more
 homogenous with a high degree of functional redundancy, despite being
 isolated from direct anthropogenic activity. 4. While taxonomic diversity
 increased over time, functional diversity has yet to catch up. These
 results demonstrate that anthropogenic pressures can remain a threat to
 biotic communities even in protected areas. The differences in taxonomic
 and functional recovery processes highlight the need to incorporate
 functional traits in assessments of biodiversity responses to global
 change.
description: Please refer to the article: Multidecadal changes in functional diversity lag behind the recovery of taxonomic diversity Nathan Jay Baker, Francesca Pilotto, Phillip J. Haubrock, Burkhard Beudert, Peter Haase Ecology & Evolution 2021
description: Please see the meta-data tab for details.
DOI: 10.5061/dryad.mgqnk9916
title: In situ hybridization probe sequences for mouse Alx3, Fgf8, Msx1, Shh, Six3

description: Serum response factor (SRF) is an essential transcription factor that
 influences many cellular processes including cell proliferation,
 migration, and differentiation. SRF directly regulates and is required for
 immediate early gene (IEG) and actin cytoskeleton-related gene expression.
 SRF coordinates these competing transcription programs through discrete
 sets of cofactors, the Ternary Complex Factors (TCFs) and Myocardin
 Related Transcription Factors (MRTFs). The relative contribution of these
 two programs to in vivo SRF activity and mutant
 phenotypes is not fully understood. To study how SRF utilizes its
 cofactors during development, we generated a
 knock-in SrfaI allele in mice harboring point mutations
 that disrupt SRF-MRTF-DNA complex formation but leave SRF-TCF activity
 unaffected. Homozygous SrfaI/aI mutants die at E10.5
 with notable cardiovascular phenotypes, and neural crest conditional
 mutants succumb at birth to defects of the cardiac outflow tract but
 display none of the craniofacial phenotypes associated with complete loss
 of SRF in that lineage. Our studies further support an important role for
 MRTF mediating SRF function in cardiac neural crest and suggest new
 mechanisms by which SRF regulates transcription during development.
description: DNA plasmids encoding in situ hybridization probes were shared
 with the Soriano lab. These were subject to Sanger sequencing using T7 and
 T3 primers. The resulting sequences were assembled into annotated .dna
 files. When a plasmid backbone was known or could be identified through
 the sequencing reads, the entire plasmid was constructed.
description: These can be read using free SnapGene software.
DOI: 10.5061/dryad.w3r2280rv
title: River network rearrangements promote speciation in lowland Amazonian birds

description: Large Amazonian rivers impede dispersal for many species, but lowland
 river networks frequently rearrange, thereby altering the location and
 effectiveness of river-barriers through time. These rearrangements may
 promote biotic diversification by facilitating episodic allopatry and
 secondary contact among populations. We sequenced genome-wide markers to
 evaluate histories of divergence and introgression in six Amazonian avian
 species-complexes. We first tested the assumption that rivers are barriers
 for these taxa and found that even relatively small rivers facilitate
 divergence. We then tested whether species diverged with gene flow and
 recovered reticulate histories for all species, including one potential
 case of hybrid speciation. Our results support the hypothesis that river
 dynamics promote speciation and reveal that many rainforest taxa are
 micro-endemic, unrecognized and thus threatened with imminent extinction.
 We propose that Amazonian hyper-diversity originates in part from
 fine-scale barrier displacement processes –including river dynamics– which
 allow small populations to differentiate and disperse into secondary
 contact.
description: The data in this dryad repository are the raw data for
 replicating analyses in <b>Musher, L.J.</b>, M. Giakoumis, J.
 Albert, G. Del Rio, M. Rego, G. Thom, A. Aleixo, C. C. Ribas, R.
 Brumfield, B.T. Smith, & J. Cracraft. River network rearrangements
 promote speciation in lowland Amazonian birds. <i>Biorxiv
 </i>https://doi.org/10.1101/2021.11.15.468717
DOI: 10.5061/dryad.dv41ns20d
title: Data from: Genotyping-in-Thousands by sequencing panel development and application to inform kokanee salmon (Oncorhynchus nerka) fisheries management at multiple scales

description: The ability to differentiate life history variants is vital for estimating
 fisheries management parameters, yet traditional survey methods can be
 inaccurate in mixed-stock fisheries. Such is the case for kokanee, the
 resident freshwater form of sockeye salmon (Oncorhynchus nerka), which
 exhibits various reproductive ecotypes (stream-, shore-, deep-spawning)
 that co-occur with each other and/or anadromous O. nerka in some systems
 across their pan-Pacific distribution. Here, we developed a multi-purpose
 Genotyping-in-Thousands by sequencing (GT-seq) panel of 288 targeted
 single nucleotide polymorphisms (SNPs) to enable accurate kokanee stock
 identification by geographic basin, migratory form, and reproductive
 ecotype across British Columbia, Canada. The GT-seq panel exhibited high
 self-assignment accuracy (93.3%) and perfect assignment of individuals not
 included in the baseline to their geographic basin, migratory form, and
 reproductive ecotype of origin. The GT-seq panel was subsequently applied
 to Wood Lake, a valuable mixed-stock fishery, revealing high concordance
 (&gt;98%) with previous assignments to ecotype using microsatellites
 and TaqMan SNP genotyping assays, while improving resolution, extending a
 long-term time-series, and demonstrating the scalability of this approach
 for this system and others.
description: Genotyping-in-Thousands by sequencing (GT-seq) following Campbell
 et al. (2015) <em>Molecular Ecology Resources</em> as modified
 in Schmidt et al. (2020) <em>Molecular Ecology
 Resources.</em>
description: 288_baseline.vcf: vcf file of genotypic data at 288 SNPs for all
 baseline individuals used for panel development 
 261_GTseq_BCnovelsamples_genepop.txt: genepop file of genotypic
 data at 261 SNPs collected with GT-seq used for panel testing
 282_GTseq_WoodLake_18_19_genepop.txt: genepop file of genotypic
 data at 282 SNPs collected with GT-seq used for Wood Lake
 application. 218_GTseq_WoodLake_12_14_genepop.txt:
 genepop file of genotypic data at 218 SNPs collected with GT-seq used for
 Wood Lake application and comparison with previous
 genotyping methods. Metadata.csv: text file containing
 individual metadata for all samples used including sample identifiers,
 location, geographic basin, reproductive ecotype, and migratory
 ecotype.
DOI: 10.5061/dryad.t1g1jwt3f
title: Impacts of male-killing Spiroplasma on the metabolic rate and ectoparasite resistance capacity (endurance) of Drosophila

description: Ectoparasitic mites are hypothesized to horizontally transmit bacterial
 endosymbionts, especially male-killing Spiroplasma. In this study we test
 how Spiroplasma poulsonii MSRO affects fly physiology and behaviour, and
 potential mite interactions.
description: We measured the metabolic rates of age-matched MSRO+ and MSRO–
 female fly cohorts at 2, 6, 11, 15, 20, 26, or 34 days post-eclosion using
 flow-through respirometry. Flies were frozen post assay, and mass was
 weighed when possible. Metabolic rate was measured as the rate of carbon
 dioxide production (uL/min). A MAVEn-FT unit was used to set the flow rate
 at 30 mL/min flow rate and control which respirometer position was active
 (14 containing flies and 1 baseline). A Li-7000 CO2 sensor was used to
 measure CO2 in air that had flown through chambers that contained MSRO+
 flies, MSRO– flies, or a baseline (empty) chamber. To improve sensitivity
 incoming air was purged of CO2 and water vapour and excurrent gas was
 purged of water vapour again using a magnesium perchlorate
 column. We used negative geotaxis endurance assays to
 measure the resistance capacity of MSRO+ and MSRO– flies. The ability to
 maintain energetically demanding activity is a proxy measure of resistance
 that eliminates the effects of mite preferences. We marked empty,
 transparent vials at 5 cm above the base, then aspirated a single MSRO+ or
 MSRO– fly into a vial and allowed 15 minutes for acclimation. At the
 outset of the experiment (t=0) the experimenter tapped the vial causing
 the fly to fall to the bottom of the vial, inducing the fly to climb. This
 knock-down procedure was repeated whenever the fly reached the 5cm line. A
 fly was considered exhausted if it failed to ascend the vial after 10
 seconds. We recorded two metrics of endurance: the number of knock-downs
 before the fly was exhausted (cycles, c), as well as the time until
 exhaustion (seconds, t); if a fly failed to climb following the initial
 knockdown both values were recorded as 0. The time it took for the fly to
 climb to the mark after the first knock-down was also recorded (first
 cycle time, f).
description: Necessary definitions are in the Meta worksheet.
DOI: 10.5061/dryad.2z34tmpnp
title: Vegetation survey data to understand drivers of plant rarity

description: Determining the drivers of plant rarity is a major challenge in ecology.
 Analysing spatial associations between different plant species can provide
 an exploratory avenue for understanding the ecological drivers of plant
 rarity. Here, we examined the different types of spatial associations
 between rare and common plants to determine if they influence the
 occurrence patterns of rare species. We completed vegetation surveys at 86
 sites in woodland, forest, and heath communities in south-east Australia.
 We also examined two different rarity measures to quantify how
 categorisation criteria affected our results. Rare species were more
 likely to have positive associations with both rare and common species
 across all three vegetation communities. However, common species had
 positive or negative associations with rare and other common species,
 depending on the vegetation community in which they occurred. Rare species
 were positively associated with species diversity in forest communities.
 In woodland communities, rare species were associated negatively with
 species diversity but positively associated with species evenness. Rare
 species with high habitat specificity were more clustered spatially than
 expected by chance. Efforts to understand the drivers of plant rarity
 should use rarity definitions that consider habitat specificity. Our
 findings suggest that examining spatial associations between plants can
 help understand the drivers of plant rarity.
description: Vegetation data were collected across Booderee National Park
 across 86 sites surveyed, across the three major vegetation communities
 across Booderee National Park. We established a 10 m by 10 m plot at each
 of the 86 sites and surveyed 100 one metre by one-metre quadrats within
 the plot by creating a ten by ten-unit grid. We identified and recorded
 the presence of all plant species within each one-metre square
 quadrat. Data were processed to calculate the number of
 rare species present at each site, using two different categorisations of
 species rarity. Species diversity, evenness and density were also collated
 at each site. Data also contains the elevation, north and east aspect of
 each site surveyed.
description: See Readme file.
DOI: 10.5061/dryad.jm63xsjcd
title: Nesting success and nesting height in the critically endangered Medium Tree Finch (Camarhynchus pauper)

description: When different introduced species across trophic levels (ectoparasite,
 predator) invade island systems, they may pose significant threats to
 nesting birds. In this study, we measure nesting height and causes of
 offspring mortality in the critically endangered Medium Tree Finch
 (Camarhynchus pauper), an island endemic restricted to Floreana Island on
 the Galápagos archipelago. Considering all nests at which a male built a
 nest, sang and attempted to attract a female (N = 222 nests), only 10.4%
 of nests produced fledglings (5% of nests had total fledging success, 5.4%
 of nests had partial fledging success). Of the 123 nests chosen by a
 female, 18.7% produced fledglings and of 337 eggs laid, 13.4% produced
 fledglings. Pairing success was higher for older males, but male age did
 not predict nesting success. All nests with chicks were infested with
 Avian Vampire Fly larvae (Philornis downsi). We attributed the cause of
 death to Vampire Fly if chicks were found dead in the nest with fly larvae
 or pupae (45%) present. We inferred avian (either Asio flammeus
 galapagoensis or Crotophaga ani) predation (24%) if the nest was empty but
 dishevelled; and Black Rat (Rattus rattus) predation (20%) if the nest was
 empty but undamaged. According to these criteria, the highest nests were
 depredated by avian predators, the lowest nests by rats, and intermediate
 nests failed because of Vampire Fly larvae. In conclusion, there is no
 safe nesting height on Floreana Island under current conditions of threats
 from two trophic levels (introduced parasitic dipteran, introduced
 mammalian/avian predators).
description: We have been monitoring nesting outcome at nests of the
 critically endangered Medium Tree Finch (Camarhynchus pauper) on Floreana
 Island, Galapagos since 2004. Nests were monitored following our
 standardised protocol that we developed in 2000 on Santa Cruz Island and
 maintained throughout the study on Floreana Island. Nests were routinely
 inspected, with binoculars and ladder during 2004 to 2006, and since 2008
 with a borescope, every three days during incubation and every two days
 during the nesting phase to confirm activity. 
description: Sheet 2 of the excel file describes each variable.
DOI: 10.15468/dl.x3wv8m
title: Occurrence Download

description: A dataset containing 380 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Cyclobalanopsis fleuryi"
 ]
}

 The dataset includes 380 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002989-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.12jm63z05
title: Cooperation of membrane-translocated syntaxin4 and basement membrane for dynamic mammary epithelial morphogenesis

description: Mammary epithelia undergo dramatic morphogenesis after puberty. During
 pregnancy, luminal epithelial cells in ductal trees are arranged to form
 well-polarized cystic structures surrounded by a myoepithelial cell layer,
 an active supplier of the basement membrane (BM). Here, we identified a
 novel regulatory mechanism involved in this process by using a
 reconstituted BM-based three-dimensional culture and aggregates of a model
 mouse cell line, EpH4, that had either been manipulated for inducible
 expression of the t-SNARE protein syntaxin4 in an intact or signal
 peptide-connected form, or that were genetically deficient in syntaxin4.
 We found that cells extruded syntaxin4 upon stimulation with the
 lactogenic hormone, prolactin, which in turn accelerated the turnover of
 E-cadherin. In response to extracellular expression of syntaxin4, cell
 populations that were less affected by the BM actively migrated and
 integrated into the cell layer facing the BM. Concurrently, the BM-facing
 cells, which were simultaneously stimulated with syntaxin4 and BM,
 acquired unique epithelial characteristics to undergo dramatic cellular
 arrangement for cyst formation. These results highlight the importance of
 the concerted action of extracellular syntaxin4 extruded in response to
 the lactogenic hormone and BM components in epithelial morphogenesis.
description: RNA-sequencing analysis was outsourced to Macrogen Japan Corp.
 (Tokyo, Japan)
description: Total RNA was extracted from EpH4 cells on collagen or Matrigel
 for three days, with or without induction of signal peptide-connected
 syntaxin4, using a Total RNA Extraction Miniprep System (VIOGENE,
 USA).