cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6071/m3fd4r
title: Files associated with: Species’ attributes predict the relative magnitude of ecological and genetic recovery following mass mortality

description: Theoretically, species’ characteristics should allow estimation of
 dispersal potential and, in turn, explain levels of population genetic
 differentiation. However, a mismatch between traits and genetic patterns
 is often reported in marine species and interpreted as evidence that
 life-history traits do not influence dispersal. Here, we couple ecological
 and genomic methods to test the hypothesis that species with attributes
 favoring greater dispersal potential — e.g. longer pelagic duration,
 higher fecundity, and larger population size — have greater realized
 dispersal overall. We used a natural experiment created by a large-scale
 and multi-species mortality event which created a ‘clean slate’ on which
 to study recruitment dynamics, thus simplifying a usually complex problem.
 We surveyed four species of differing dispersal potential to quantify the
 abundance and distribution of recruits and to genetically assign these
 recruits to likely parental sources. Species with higher dispersal
 potential re-colonized a broader extent of the impacted range, did so more
 quickly, and recovered more genetic diversity than species with lower
 dispersal potential. Moreover, populations of taxa with higher dispersal
 potential exhibited more immigration (71–92% of recruits) than taxa with
 lower dispersal potential (17–44% of recruits). By linking ecological with
 genomic perspectives, we demonstrate that a suite of interacting life
 history and demographic attributes do influence species’ realized
 dispersal and genetic neighborhoods. To better understand species’
 resilience and recovery in this time of global change, integrative
 eco-evolutionary approaches are needed to more rigorously evaluate the
 effect of dispersal-linked attributes on realized dispersal and population
 genetic differentiation.
description: See publication.
DOI: 10.5061/dryad.c2fqz61c7
title: Piezo1 as a force-through-membrane sensor in red blood cells

description: Piezo1 is the stretch-activated Ca2+ channel in red blood cells that
 mediates homeostatic volume control. Here we study the organization of
 Piezo1 in red blood cells using a combination of super-resolution
 microscopy techniques and electron microscopy. Piezo1 adopts a nonuniform
 distribution on the red blood cell surface, with a bias towards the
 biconcave "dimple". Trajectories of diffusing Piezo1 molecules,
 which exhibit confined Brownian diffusion on short timescales and hopping
 on long timescales, also reflect a bias towards the dimple. This bias can
 be explained by "curvature coupling" between the intrinsic
 curvature of the Piezo dome and the curvature of the red blood cell
 membrane. Piezo1 does not form clusters with itself, nor does it
 co-localize with F-actin, Spectrin or the Gardos channel. Thus, Piezo1
 exhibits the properties of a force-through-membrane sensor of curvature
 and lateral tension in the red blood cell.
DOI: 10.25338/b8963g
title: Sunflower consensus scoring

description: Biological rhythms are ubiquitous. They can be generated by circadian
 oscillators, which produce daily rhythms in physiology and behavior, as
 well as by developmental oscillator such as the segmentation clock, which
 produces modular developmental units in a periodic fashion. Here, we show
 that the circadian clock controls the timing of late-stage floret
 development, or anthesis, in domesticated sunflower. In these plants, what
 appears to be a single inflorescence consists of up to thousands of
 individual florets tightly packed onto a capitulum disk. While early
 floret development occurs continuously across capitula to generate iconic
 spiral phyllotaxy, during anthesis floret development occurs in discrete
 ring-like pseudowhorls with up to hundreds of florets undergoing
 simultaneous maturation. We demonstrate circadian regulation of floral
 organ growth and show that the effects of light on this process are
 time-of-day dependent. Disruption of circadian rhythms in floral organ
 development causes loss of pseudowhorl formation. Thus, we show that the
 sunflower circadian clock acts in concert with environmental response
 pathways to tightly synchronize the anthesis of hundreds of florets each
 day, generating spatial patterns on the developing capitulum disk. This
 coordinated mass release of floral rewards at predictable times of day
 likely promotes pollinator visits and plant reproductive success.
description: The
 15-minute interval images were analyzed sequentially in a stack on ImageJ.
 A clockwise parastichy was selected, and florets numbered from the outer
 edge of the pseudowhorl inward. At images taken at 15-minute intervals,
 the ovaries, stamens, and styles for each floret were scored for a change
 in size from the previous image. Four parastichies per condition were
 analyzed, from two different sunflower heads. In LL|25°C conditions, which
 had no pseudowhorls, 10 florets in a parastichy were scored for 48 hours.
 For all other conditions tested, a parastichy from the
 2<sup>nd</sup> pseudowhorl was scored until anthesis of all
 florets per parastichy within the pseudowhorl was complete. For the
 DD|25°C condition, the 4<sup>th</sup> pseudowhorl was also
 scored.
description: Microsoft Excel
DOI: 10.5061/dryad.0k6djhb38
title: Genome-wide analysis resolves the radiation of New Zealand’s freshwater Galaxias vulgaris complex and reveals a candidate species obscured by mitochondrial capture

description: Aim: Freshwater fish radiations are often characterized by multiple
 closely-related species in close proximity, which can lead to
 introgression and associated discordance of mitochondrial and nuclear
 characterizations of species diversity. As a case in point, single locus
 nuclear versus mitochondrial analyses of New Zealand’s stream-resident
 Galaxias vulgaris complex have yielded conflicting phylogenies. Our goal
 is to use genome-wide divergence patterns among these fishes to evaluate
 the potential role of mitochondrial capture in obscuring species diversity
 and to understand how ancient and anthropogenic drainage modification
 explains this diversity. Location: Freshwater ecosystems of New Zealand.
 Methods: We generate and analyze a genome-wide data set comprising 52,352
 SNPs across 187 Galaxias specimens to resolve the phylogeny of this recent
 fish radiation. We conduct phylogenetic, PCA, STRUCTURE, and ABBA-BABA
 analyses to evaluate the evolutionary relationships of lineages in the
 context of natural and anthropogenic river drainage alterations. Results:
 In addition to the 11 previously recognized stream-resident lineages,
 genome-wide data reveal a twelfth candidate species (G. ‘Pomahaka’),
 apparently obscured by introgressive mitochondrial capture. We identify
 additional examples of mito-nuclear discordance and putative mitochondrial
 capture, likely mediated by geological and anthropogenic modification of
 drainage boundaries. Main conclusions: Our study highlights the need for
 genome-wide approaches for delimiting freshwater biodiversity. Genetic
 data also reveal the influence of drainage history on freshwater
 biodiversity, including the rapid divergence of recently fragmented fish
 populations, and the conservation genetic risks of anthropogenic
 translocations events.
description: This is a dataset of 187 <em>Galaxias</em> sp. from
 across their range in Aotearoa New Zealand. They have been sequenced using
 Genotyping by-Sequencing, a variant of RAD-Seq. For detailed methods,
 please refer to the README and the script. Do not hesitate to contact the
 authors.
description: This folder includes the main script used to go from raw data to
 SNPs, as well as the code used to produce the phylogenetic tree.
 The demultiplexed data can be obtained from the
 Short-Read-Archive as specified in the article. For any
 questions, please do not hesitate to contact Ciaran Campbell (ciarancampbell10@gmail.com) or Ludovic Dutoit (ludovic.dutoit@otago.ac.nz).
DOI: 10.5061/dryad.sxksn036g
title: Alpine climate and soils heterogeneity data and simulation results

description: We developed metrics of climatic and edaphic heterogeneity, using
 principal components analyses and the shoelace algorithm, and added
 elevation range. We applied commonality analysis to partition the unique
 and shared explanation of the observed vascular plant species richness
  among selected metrics. A simulation was developed to separate
 the relative importance of area and heterogeneity at different extents and
 representations of spatial nestedness, and the heterogeneity – effective
 area tradeoff was evaluated by altering spatial discreteness. The
 simulations revealed that heterogeneity was consistently more important,
 but less so among smaller areas. This qualitative pattern was maintained
 regardless of whether and how nestedness was represented. The
 heterogeneity – effective area tradeoff occurred in a few simulations of
 more discrete habitats.
description: Data for 8 climate variables from CHELSA and 11 soils variables
 from ISRIC (uppermost layer only) were used to produce metrics of
 environmental heterogeneity. The first two axes were used to plot the
 points for each of the 23 regions in 2D PCA (PC-ORD v7) space. Between 5
 and 15 points that outlined the area occupied by the points were selected
 to create a polygon, and the shoelace algorithm was applied to them to
 calculate the area. The data show the two PCA axes split out for each
 region, the points selected for the shoelace calculation, and the area. In
 some cases where the points were in two distinct clusters the areas were
 measured separately and summed. The complete CHELSA
 data are available at Dryad: http://dx.doi.org/doi:10.5061/dryad.kd1d4. The ISRIC data are available at https://www.isric.org/explore/isric-soil-data-hub under ISRIC’s own applicable access categories: CC-BY-NC and CC-BY, and their policies are described at https://www.isric.org/about/data-policy The data from CHELSA and ISRIC are not included here. Only the results of the PCA that used those data are in this submission to Dryad. A simulation model was developed in NetLogo for computational experiments. The treatment parameters were environmental heterogeneity and area, and 10 random number seeds were used to create replications. The output was regional species richness, i.e., the number of species extant on the grid at equilibrium. The explanation of the observed regional richness was shared by area and heterogeneity. 
description: Excel can be used to access the data file. Alternatively, files
 can also be accessed using Apache OpenOffice.
DOI: 10.5061/dryad.2547d7wtm
title: Eusocial evolution without a nest: kin structure of social aphids forming open colonies on bamboo

description: Living in nests is an almost universal feature of eusocial animals. In
 some aphids, however, sterile soldier castes have evolved in open colonies
 without a nest. To clarify the factors promoting the evolution of
 eusociality in these colonies, we used newly developed microsatellite
 markers to compare the kin structure of the open colonies of two aphid
 species on bamboo: the non-eusocial colonies of Astegopteryx
 bambucifoliae and the eusocial colonies of Pseudoregma
 alexanderion Dendrocalamus latiflorus. Our samples, from
 over 1,000 hectares, contained 99 clones of A. bambucifoliae and
 19 of P. alexanderi. Clonal mixing occurred in both species:
 average pairwise relatedness within a colony was 0.54 in A.
 bambucifoliae and 0.71 in P. alexanderi. Each clone
 of A. bambucifoliae occurred in a unique location,
 whereas those of P. alexanderi occurred in multiple locations and
 more than 90% of individuals came from just four clones. There was
 significant genetic variation among different colonies in the same clump
 (stem-cluster) in A. bambucifoliae but not
 in P. alexanderi, indicating that P.
 alexanderi colonies in a single clump are
 genetically homogenized, functioning as a large colony. In P.
 alexanderi, the proportion of sterile soldiers to normal first-instar
 nymphs was significantly different across the four clones. Our
 results indicate that the lack of input of migrants from the primary host
 and feeding on a large, stable host plant are important ecological factors
 that might favour the evolution of eusociality, enabling the production of
 genetically homogenised, large, and long-lived colonies. After eusociality
 evolves on the secondary host, the optimal strategy of soldier production
 might vary between different clones.
DOI: 10.5061/dryad.r4xgxd2gj
title: Phylogenomics reveal extensive phylogenetic discordance due to incomplete lineage sorting following the rapid radiation of alpine butterflies (Papilionidae: Parnassius)

description: In rapid radiation, the earliest components of evolutionary divergence are
 often difficult to resolve, which were always driven by the
 characteristics of taxa and the limitations of alternative analytical
 methods. The origin and radiation of the alpine butterfly
 Parnassius, a high-altitude mountainous insect group, can be attributed to
 the uplift of the Qinghai-Tibet Plateau (QTP). Despite detailed
 phylogenetic analyses of the genus, deep phylogenetic relationships among
 the major subgenera remain recalcitrant. In this study, 102 individuals
 from 10 representative Parnassius species were sampled to resolve the
 phylogenetic relationships among subgenera based on nuclear and
 mitochondrial genome data sets. Gene-tree/species-tree conflicts were
 detected by concatenation and multispecies coalescent (MSC) approaches. We
 recovered a well-supported species tree, despite these conflicts, and
 detected considerable phylogenetic discordance among genomic regions. The
 main explanation for the topological discordance among subgenera was
 extensive incomplete lineage sorting (ILS), whereas introgression events
 were not prominent. The origin and explosive radiation of Parnassius
 (i.e., rapid succession of speciation events) in the late Miocene
 associated with environmental events on the plateau led to short internal
 branches, thereby increasing ILS and topological conflicts, especially
 among closely related subgenera. Our results also suggested that MSC
 approaches (SNAPP and SVDquartets) are accurate and superior to the
 concatenation approach; in particular, SVDquartets can explicitly
 accommodate gene-tree/species-tree conflicts caused by high ILS and
 demonstrate strong robustness. Lastly, we explored the phylogenomic data
 by testing multiple sources of phylogenomic conflict to clarify the
 strengths and limitations of different approaches, while considering
 phylogenetic signal variation in mitochondrial loci. We anticipate that
 the phylogeny described here will be the backbone of future evolutionary
 studies of the genus and will provide insight into phylogenetic
 discordance due to rapid radiation.
DOI: 10.5061/dryad.mw6m9060b
title: Trait adaptation enhances species coexistence and reduces bistability in an intraguild predation module

description: Disentangling how species coexist in an intraguild predation (IGP) module
 is a great step towards understanding biodiversity conservation in complex
 natural food webs. Trait variation enabling individual species to adjust
 to ambient conditions may facilitate coexistence. However, it is still
 unclear how co-adaptation of all species within the IGP module,
 constrained by complex trophic interactions and trade-offs among
 species-specific traits, interactively affects species coexistence and
 population dynamics. We developed an adaptive IGP model allowing prey and
 predator species to mutually adjust their species-specific defensive and
 offensive strategies to each other. We investigated species persistence,
 the temporal variation of population dynamics, and the occurrence of
 bistability in IGP models without and with trait adaptation along a
 gradient of enrichment represented by carrying capacity of the basal prey
 for different widths and speeds of trait adaptation within each species.
 Results showed that trait adaptation within multiple species greatly
 enhanced the coexistence of all three species in the module. A larger
 width of trait adaptation facilitated species coexistence independent of
 the speed of trait adaptation at lower enrichment levels, while a
 sufficiently large and fast trait adaptation promoted species coexistence
 at higher enrichment levels. Within the oscillating regime, increasing the
 speed of trait adaptation reduced the temporal variability of biomasses of
 all species. Finally, species co-adaptation strongly reduced the presence
 of bistability and promoted the attractor with all three species
 coexisting. These findings resolve the contradiction between the
 widespread occurrence of IGP in nature and the theoretical predictions
 that IGP should only occur under restricted conditions and lead to
 unstable population dynamics, which broadens the mechanisms presumably
 underlying the maintenance of IGP modules in nature. Generally, this study
 demonstrates a decisive role of mutual adaptation among complex trophic
 interactions, for enhancing interspecific diversity and stabilizing food
 web dynamics, arising e.g. from intraspecific diversity.
description: See manuscript for details.
DOI: 10.5061/dryad.sqv9s4n6q
title: Plant growth over one growing season of Medicago truncatula in competition with conspecifics of different genetic relatedness

description: Kin recognition and kin selection have long been known to occur in animals
 where it shapes altruistic behavior towards relatives. More recently,
 studies have found that kin recognition and altered behavior towards kin
 can also occur in plants. However, inferring the underlying mechanism
 responsible for variation in plant performance in experimental studies is
 challenging as often, results can be explained by alternative and
 non-exclusive mechanisms such as niche differences, kin competition
 avoidance, and genetic variation in growth rate and competitive ability.
 Plant-plant interactions may change with the life stage of plants, and
 competition is often most intense towards the end of plants growing
 season. However, changes in plant-plant interaction intensity across
 plants life cycle are rarely considered in kin interaction studies. Here,
 we adapt a model of plant growth over time modified to specifically
 include effects of kin and non-kin competition. The model decompose
 competitive interactions at different stages during plant growth from
 initial growth to the end of the growing season. It estimates genotype
 specific variation in growth rate, and how sensitive individual genotypes
 are to competition  neighbors. Furthermore, it estimates size
 asymmetry among plants accounting for both variation in growth rate,
 neighbor relatedness, and resource variation (here water availability). We
 use this model to analyze the results from a competition experiment where
 plants grew in mini-communities with neighbor plants that were either kin
 or non-kin. We find that when applied to our experiments, this approach
 can disentangle kin effects from other effects caused by genotypic
 variation in growth rate and competitive response to neighbors, and thus
 significantly help to detect whether plants exhibit kin-cooperative
 behavior
DOI: 10.5061/dryad.r7sqv9sg3
title: Disentangling direct and indirect drivers of farmland biodiversity at landscape scale

description: To stop the ongoing decline of farmland biodiversity there are increasing
 claims for a paradigm shift in agriculture, namely from conserving and
 restoring farmland biodiversity at field scale (α-diversity) to doing it
 at landscape scale (γ-diversity). However, knowledge on factors driving
 farmland γ-diversity is currently limited. Here, we quantified farmland
 γ-diversity in 123 landscapes and analysed direct and indirect effects of
 abiotic and land-use factors shaping it using structural equation models.
 The direction and strength of effects of factors shaping γ-diversity were
 only partially consistent with what is known about factors shaping
 α-diversity, and indirect effects were often stronger than direct effects
 or even opposite. Thus, relationships between factors shaping α-diversity
 cannot simply be up-scaled to γ-diversity, and also indirect effects
 should no longer be neglected. Finally, we show that local mitigation
 measures benefit farmland γ-diversity at landscape scale and are therefore
 a useful tool for designing biodiversity-friendly landscapes. 
description: We sampled the farmland in 123 study
 squares of 1 km<sup>2</sup> each in Switzerland between 2015
 and 2019. The dataset contains for the farmland per
 square: - species richness of plants
 (Plant_GAMM) - species richness of butterflies
 (Butt_GAMM) - species richness of birds
 (Bird_GAMM) - multitrophic species richess
 (multitrophic_speciesrichness) - percentage cover of plants with low
 dispersal ability (Plant_ShortDisp_abu)
 - percentage cover of plants with high
 dispersal ability (Plant_LongDisp_abu)
 - abundance of food-specialized
 butterflies (Butt_FoodSpec_abu) - abundance of food non-specialized
 butterflies (Butt_FoodGen_abu) - abundance of migration-limited birds
 (Bird_ShortMig_abu) - abundance of migration non-limited
 birds (Bird_LongMig_abu) - mean slope (slope)
 - mean yearly precipitation days
 (pday) - mean annual degree-days
 (ddeg) - share of farmland
 (perc_farmland) - share of land-use class “arable”
 (perc_arable) - share of land-use class “wood”
 (perc_wood) - mean land-use intensity index derived from habitat
 types (LUI_index) - number of detailed land-cover types
 (LC_richness) - interspersion (spatial intermixing) of the detailed
 land cover types (LC_interspersion)
 - share of grass EFAs
 (EFA_perc_grass) - share of arable EFAs
 (EFA_perc_arable) - share of wood EFAs
 (EFA_perc_wood) - number of different EFA types
 (EFA_types) - mean EFA patch size
 (EFA_size) - mean nearest distance between EFA patches (EFA
 distance) Based on this data, additionally an R script is
 included to check for multicollinearity and to generate the SEMs in the
 article. 
description: R
DOI: 10.15468/dl.9rh9jd
title: Occurrence Download

description: A dataset containing 581 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-49.56908 15.47368,62.83224 15.47368,62.83224 60.47368,-49.56908 60.47368,-49.56908 15.47368))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Eichhornia crassipes"
 ]
}

 The dataset includes 581 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003230-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.