cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pzgmsbcmt
title: Sexual selection and the population genetics of a selfish gene

description: The segregation distorter allele (SD) found in Drosophila melanogaster
 distorts Medelian inheritance in heterozygous males by causing
 developmental failure of non-SD spermatids, such that &gt;90% of the
 surviving sperm carry SD. This within-individual advantage should cause SD
 to rapidly fix, and yet SD is typically rare in wild populations. Here, we
 explore whether this paradox can be resolved by sexual selection, by
 testing if males carrying three different variants of SD suffer reduced
 pre or postcopulatory reproductive success. We find that males carrying
 the SD allele are just as successful at securing matings as control males,
 but that one SD variant (SD-5) reduces sperm competitive ability and
 increases the likelihood of female remating. We then used these results to
 inform a theoretical model; we found that sexual selection could limit SD
 to the frequencies observed in nature when sperm competitive ability and
 female remating rate equalled the values observed for SD-5. However,
 sexual selection was unable to explain natural frequencies of the SD
 allele when the model was parameterized with the values found for two
 other SD variants, indicating that sexual selection alone is unlikely to
 explain the rarity of SD.
description: This data was collected during laboratory experiments using
 <em>Drosophila melanogaster</em>. It has been used in the
 manuscript titled "Sexual selection and the population genetics of a
 selfish gene", to be published in <em>Proceedings of the Royal
 Society B</em>. 
 See https://tomkeaney.github.io/SD_sexual_selection/Empirical_analysis.html for a detailed description of the three datasets. A description is also included in the attached README file.
DOI: 10.5068/d1v966
title: PacBio sequencing output increased through uniform and directional 5-fold concatenation

description: Advances in sequencing technology have allowed researchers to sequence DNA
 with greater ease and at decreasing costs. Main developments have focused
 on either sequencing many short sequences or fewer large sequences.
 Methods for sequencing mid-sized sequences of 600-5,000 bp are currently
 less efficient. For example, the PacBio Sequel I system yields
 ~100,000-300,000 reads with an accuracy per base pair of 90-99%. We sought
 to sequence several DNA populations of ~870 bp in length with a sequencing
 accuracy of 99% and to the greatest depth possible. We optimised a simple,
 robust method to concatenate genes of ~870 bp five times and then
 sequenced the resulting DNA of ~5,000 bp by PacBioSMRT long-read
 sequencing. Our method improved upon previously published concatenation
 attempts, leading to a greater sequencing depth, high-quality reads and
 limited sample preparation at little expense. We applied this efficient
 concatenation protocol to sequence nine DNA populations from a protein
 engineering study. The improved method is accompanied by a simple and
 user-friendly analysis pipeline, DeCatCounter, to sequence medium-length
 sequences efficiently at one-fifth of the cost.
description: Sequencing data: Dataset with 12,505 amplicons, corresponding to
 a subset of the raw dataset analyzed in the publication (124,715
 amplicons): dataset.fasta Barcodes: Barcode sequences
 used for demultiplexing: barcodes.txt Constant regions:
 Constant region sequences used for deconcatenating: constant.txt
 DeCatCounter: Python script to demultiplex the amplicons,
 deconcatenatenate into sequences and count their count reads:
 DeCatCounter.py Count files: Text files with amino acid
 sequences read counts for the nine rounds of selection. Each file contains
 round information (number of unique sequences and total number of
 molecules) in its header, followed by sequences and the number of times
 they appeared in that round. Sequences have been labelled using the code
 “sequence_X”, where X corresponds to the order in which the sequence
 appears in the files: count_files.zip
DOI: 10.5061/dryad.pnvx0k6n9
title: Data from: Trophic strategies of two sympatric endemic pigeons in insular ecosystems: a framework for understanding spatiotemporal frugivory interactions

description: Pigeons are considered to play key ecological roles in frugivory and seed
 dispersal. They have colonised numerous oceanic islands and diversified
 into several species in sympatry. How these species coexist in similar
 niches is poorly understood, although dietary separation is among the
 mechanisms suggested to avoid trophic overlap. We investigated the trophic
 ecology of the two endemic Columba species co-occurring in the laurel
 forest and thermosclerophyllous relicts of two of the Canary Islands. This
 study includes diet description in spatiotemporal terms, its relationship
 with fruit availability, and seed treatment in ten study areas established
 on La Palma and La Gomera. We used non-invasive DNA analysis to identify
 the faeces of the two congeneric species and microhistological methods to
 examine their diets. The degree of trophic overlap was evaluated by niche
 similarity and breadth indices. Molecular faecal sampling determined the
 spatiotemporal distribution of both pigeons to identify their areas of
 coexistence. These frugivorous pigeons' diets did not differ
 concerning the main plant species, but they diverged quantitatively in the
 proportions and parts of plants consumed. Lauraceae fruits were their
 staple foods, although Rhamnaceae and some Fabaceae and Solanaceae were
 also important. Both pigeons showed selective preferences for some fruits.
 Significant spatiotemporal variations in their diets were observed along
 with a general tendency to increase fruit intake at its ripening times.
 Our results suggest that different trophic strategies facilitate the
 coexistence of these frugivorous columbids. These pigeons act as seed
 dispersers and/or predators depending on seed features (size and
 hardness), and this may have valuable implications for their conservation.
DOI: 10.5061/dryad.dz08kprz5
title: Data from: Identifying extracellular vesicles from single cells

description: Extracellular vesicles (EVs) are constantly secreted from both eukaryotic
 and prokaryotic cells. EVs, including those referred to as exosomes, may
 have an impact on cell signaling and an incidence in diseased cells. In
 this manuscript, a platform to capture, quantify, and phenotypically
 classify the EVs secreted from single cells is introduced. Microfluidic
 chambers of about 300 pL are employed to trap and isolate
 individual cells. The EVs secreted within these chambers are then captured
 by surface-immobilized monoclonal antibodies (mAbs), irrespectively of
 their intracellular origin. Immunostaining against both plasma-membrane
 and cytosolic proteins was combined with highly sensitive, multi-color
 total internal reflection fluorescence microscopy (TIRFM) to characterize
 the immobilized vesicles. The data analysis of high-resolution images
 allowed the assignment of each detected EV to one of 15 unique
 populations, and demonstrated the presence of highly-heterogeneous
 phenotypes even at the single-cell level. The analysis also revealed that
 each mAb isolates phenotypically-different EVs, and more vesicles were
 effectively immobilized when CD63 was targeted instead of CD81. Finally,
 we demonstrate how an heterogeneous suppression in the secreted vesicles
 is obtained when the enzyme neutral sphingomyelinase is inhibited.
description: Images of immobilized extracellular vesicles on a microfluidic
 device were recorded by use of multi-color total internal fluorescence
 microscopy (TIRFM) as described in the manuscript. Images were analyzed by
 a Matlab script as described in the data file
 "live_script_01.pdf". The compressed file
 "figure-excel-files" contains the results used to create the
 final graphs in figures 3, 4, 5 and 6. The compressed
 file "matlab_analysis_script" contains the image analysis file
 and example figures.
DOI: 10.5061/dryad.0gb5mkm1t
title: Afrotropical secondary forests exhibit fast diversity and functional recovery, but slow compositional and carbon recovery after shifting cultivation

description: Question: Human disturbance is increasingly affecting forest dynamics
 across the tropics. Forests can recover via natural secondary succession
 to pre-disturbance levels of biodiversity, species composition, and
 ecosystem carbon stocks. Central Africa will be subject to increasingly
 high shifting cultivation pressure in the next decades, but succession
 trajectories of these ecosystem properties are still poorly known for the
 Congo basin. We addressed two questions: (1) how does taxonomic and
 functional composition and diversity shift? (2) How fast do aboveground
 carbon stocks recover during secondary succession in tropical forests?
 Location: Central Congo basin Methods: We conducted an inventory of trees
 (DBH ≥10 cm diameter), measured species traits and soil texture and carbon
 content in 18 plots, located along six secondary succession stages (i.e.
 from agricultural to old growth forest sites). We measured tree diameter,
 height for 20% of trees distributed across diameter classes, wood traits
 from all species, and leaf traits from species that contributed to 85% of
 the plot basal area. Results: We showed that secondary forests recover
 relatively fast in terms of tree species diversity, alpha functional
 diversity, and fine root carbon, with near-old-growth forest values after
 six decades past disturbance, while floristic composition exhibited slower
 recovery. Secondary forests only partially shifted from acquisitive to a
 conservative life-history, with shifts in leaf traits being largely
 decoupled from wood traits. Only 43% of above-ground carbon recovered
 after 60 years of forest regrowth, potentially through a slow recovery of
 the large-sized tree stems that dominate carbon stocks of old-growth
 forests. Conclusions: Our findings underline the capacity of Afrotropical
 forests to recover species and alpha functional diversity after
 clear-cutting through shifting cultivation. Simultaneously, old-growth
 forests harbors a particular floristic community and store a large
 quantity of carbon with much longer recovery trajectories, stressing the
 need for conservation of these forests in the Congo Basin.
DOI: 10.5061/dryad.9p8cz8wh0
title: Data used in timing is everything: Dichogamy and pollen germinability underlie variation in autonomous selfing among populations

description: Premise of the study: The evolution of multiple floral traits
 often underlies the transition from outcrossing to selfing. Such traits
 can influence the ability to self, and the timing at which selfing occurs,
 which in turn affects the costs of selfing. Species that display variation
 in autonomous selfing provide an opportunity to dissect the phenotypic
 changes that contribute to variability in the mating system. 
 Methods: In a common garden, we measured dichogamy and herkogamy
 in 24 populations of the protandrous mixed-mating herb Campanula
 americana, and related these to autonomous fruit set (autonomy).
 We then measured the timing of self-pollen deposition and fruit production
 in populations with high and low autonomy, and determined whether pollen
 germinability across floral development contributes to variation in
 autonomy.  Key Results: Populations that transitioned
 more rapidly to female phase displayed elevated autonomous selfing, but
 herkogamy was unassociated with autonomous selfing. Selfing occurred more
 rapidly in highly-autonomous populations due to greater self-pollen
 deposition early in female phase. Pollen germinability in low-autonomy
 populations remained constant across floral development, but in
 high-autonomy populations it increased after floral anthesis and was
 highest near the onset of female phase. 
 Conclusions: Reduced dichogamy, elevated self-pollen deposition,
 and higher pollen germination late in male phase contribute to both
 earlier selfing and greater selfing. These traits vary among populations,
 likely reflecting past selection on the mating system. While delayed
 selfing bears fewer fitness costs, the evolution of earlier selfing may be
 favored if self-pollen availability decreases over floral development.
description: Data was collected from Campanula americana plants growing in the
 greenhouse. Plant growth and data collection methods are detailed in the
 paper. The files include raw data. 
description: Each excel file has one sheet that contains the data and another
 sheet that contains the metadata, describing the data under each
 header.<br> In each data set, each ID is a different plant. The
 files "TimingOfSelfing_FOR UPLOAD" and
 "Individ_GHData_AutHerkDich FOR UPLOAD" contain missing data.
 Missing data resulted because not all variables were measured on each
 plant. Missing data is indicated by 'n/a'.
DOI: 10.5061/dryad.bk3j9kdcr
title: The color of greater flamingo feathers fades when no cosmetics are applied

description: Greater flamingos use cosmetic coloration by spreading uropygial
 secretions pigmented with carotenoids over their feathers, which makes the
 plumage redder. Because flamingos inhabit open environments that receive
 direct solar radiation during daytime, and carotenoids bleach when exposed
 to solar radiation, we expected that the plumage color would fade if there
 is no maintenance for cosmetic purposes. Here, we show that the
 concentrations of pigments inside feathers and on the surface of feathers
 were correlated, as well as that there was a correlation between the
 concentrations of pigments in the uropygial secretions and on the surface
 of feathers. There was fading in color (becoming less red) in feathers
 that received direct solar radiation when there was no plumage
 maintenance, but not so in others maintained in darkness. When we
 controlled for the initial color of feathers, the feathers of those
 individuals with higher concentration of pigments on the feather surfaces
 were those that lost less coloration after experimental exposure of
 feathers to sunny conditions. These results indicate that exposure to
 sunlight is correlated with the fading of feather color, which suggests
 that individuals need to regularly apply make-up to be more colorful.
 These results also reinforce the view that these birds use cosmetic
 coloration as a signal amplifier of plumage color. This may be important
 in species using highly variable habitats, such as wetlands, since the
 conditions experienced when molting may differ from those when the signal
 should be functional, usually months after molting.
DOI: 10.5061/dryad.qjq2bvqgr
title: Data from: Coastal darkening substantially limits the contribution of kelp to coastal carbon cycles

description: Macroalgal-dominated habitats are rapidly gaining recognition as important
 contributors to marine carbon cycles and sequestration. Despite this
 recognition, relatively little is known about the production and fate of
 carbon originating from these highly productive ecosystems, or how
 anthropogenic and climate related stressors affect the role of macroalgae
 in marine carbon cycles. Here, we examine the impact of increasing
 turbidity on carbon storage, fixation and loss in southern hemisphere kelp
 forests. We quantified net primary production (NPP) and biomass
 accumulation (BA), and estimated carbon release via detritus and dissolved
 organic carbon (DOC) across a large-scale turbidity gradient. We show that
 increased turbidity, resulting in a 63 % reduction in light, can result in
 a 95 % reduction in kelp productivity. When averaged annually, estimates
 of NPP and BA per plant at high light sites were nearly 6 and 2 times
 greater than those at low light sites, respectively. Furthermore, the
 quantity of carbon fixed annually by kelp forests was up to 4.7 times
 greater than that stored as average annual standing stock. At low light
 sites, the majority of C goes directly into tissue growth and is
 subsequently eroded. In contrast, excess production at high light sites
 accounts for up to 39 % of the total carbon fixed and is likely released
 as DOC. Turbidity is expected to increase in response to climate change
 and our results suggest this will have significant impacts on the capacity
 of kelp forests to contribute to carbon sequestration pathways. In
 addition to demonstrating that turbidity significantly reduces the
 quantity of carbon fixed by kelp forests, and subsequently released as
 detritus, our results highlight the negative impacts of turbidity on a
 large source of previously unaccounted for carbon.
description: <strong>Blain_GCB2021_data</strong>
 This file contains eight datasets which were used in the analysis
 of the manuscript: 1) average seasonal photosynthetic parameters for each
 site used in the model of NPP, 2) average environmental parameters used
 for DistLM analyses, 3) average seasonal C/N content of kelp at each site,
 4) average seasonal estimates of BA and NPP at each site, 5) average rate
 of tissue erosion at each site in each season and corresponding days
 between sampling, 6) data for analysis of plant mortality in each season
 at each site, and 7) annual average estimates of carbon production and
 export for each site.
DOI: 10.5061/dryad.d51c5b03v
title: Morphological data quantifying sexual dimorphism of Anolis carolinensis in presence and absence of congener

description: Natural selection favors sexual dimorphism that reduces resource
 competition between the sexes of the same species. However, niche
 partitioning among interspecific competitors should counter such
 divergence, as partitioning the niche results in smaller total niche
 widths for each individual species, leaving less room for the sexes to
 diverge. A straightforward (and long-standing) hypothesis emerges: species
 in competitor-rich ecological communities should show less sexual
 dimorphism than species in competitor-poor ecological communities. Here,
 we test this prediction using a well-documented natural experiment
 generated by the recent arrival of Anolis sagrei to a set of small islands
 in Mosquito Lagoon, Florida, containing Anolis carolinensis. Despite known
 interspecific habitat partitioning and rapid evolution in habitat-use
 traits by A. carolinensis in this system, sexual dimorphism between male
 and female A. carolinensis was not reduced as predicted on two-species
 islands relative to islands with only A. carolinensis. This is consistent
 with a small but growing body of empirical tests of the
 dimorphism-richness hypothesis that have been ambiguous in their support
 at best. A rethinking of the validity of this intuitive hypothesis is
 needed.
description: See details in the Methods section of main paper. See Stuart et
 al., 2014, Science 346: 463-466 and its supporting information for
 coordinates of island location. Outlier detection was
 performed with outlier defined as values &gt; 3 standard deviations
 from the mean for a given island (see 1.data.manip.R). For individuals
 with many outliers in the size corrected, the size (SVL) data were checked
 against the original data sheet and corrected where errors were detected
 in data entry. A small number of individuals were detected with one or two
 outliers which is to be expected given the large data set used. One
 individual with nine outliers was excluded from the analysis.
description: README file included.
DOI: 10.5061/dryad.xksn02vgn
title: Genomic assessment of global population structure in a highly migratory and habitat versatile apex predator, the tiger shark (Galeocerdo cuvier)

description: Understanding the population dynamics of highly mobile, widely
 distributed, oceanic sharks, many of which are overexploited, is necessary
 to aid their conservation management.  We investigated the global
 population genomics of tiger sharks (Galeocerdo cuvier), a circumglobally
 distributed, apex predator displaying remarkable behavioral versatility in
 its diet, habitat use (near coastal, coral reef, pelagic), and individual
 movement patterns (spatially resident to long-distance migrations).
  We genotyped 242 tiger sharks from 10 globally distributed
 locations at more than 2000 single nucleotide polymorphisms. Although this
 species often conducts massive distance migrations, the data show strong
 genetic differentiation at both neutral (FST=0.125-0.144) and candidate
 outlier loci (FST=0.570-0.761) between western Atlantic and Indo-Pacific
 sharks, suggesting the potential for adaptation to the environments
 specific to these oceanic regions. Within these regions, there
 was mixed support for population differentiation between northern and
 southern hemispheres in the western Atlantic, and none for structure
 within the Indian Ocean. Notably, the results demonstrate a low level of
 population differentiation of tiger sharks from the remote Hawaiian
 archipelago compared to sharks from the Indian Ocean (FST=0.003-0.005,
 P&lt;0.01). Given concerns about biodiversity loss and marine
 ecosystem impacts caused by overfishing of oceanic sharks in the midst of
 rapid environmental change, our results suggest it imperative that
 international fishery management prioritize conservation of the
 evolutionary potential of the highly genetically differentiated Atlantic
 and Indo-Pacific populations of this unique apex predator. Furthermore, we
 suggest targeted management attention to tiger sharks in the Hawaiian
 archipelago based on a precautionary biodiversity conservation
 perspective.
description: Genotyping-by-Sequencing library preparation was performed per
 Elshire et al. (2011) and raw sequence reads were generated on an Illumina
 HiSeq.
description: These data were sequenced on three Illumina HiSeq lanes, and the
 data from each lane has been split into two separate fq.gz files for
 upload (i.e., split1, and split2). Key file associating
 barcodes with sample IDs included.