cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.np5hqbzq8
title: Data from: Sibling rivalry vs mother’s curse: can kin competition facilitate a response to selection on male mitochondria?

description: Assuming that fathers never transmit mitochondrial DNA (mtDNA) to their
 offspring, mitochondrial mutations that affect male fitness are invisible
 to direct selection on males, leading to an accumulation of male-harming
 alleles in the mitochondrial genome (mother’s curse). However, male
 phenotypes encoded by mtDNA can still undergo adaptation via kin selection
 provided that males interact with females carrying related mtDNA, such as
 their sisters. Here, using experiments with Drosophila melanogaster
 carrying standardised nuclear DNA but distinct mitochondrial DNA, we test
 whether the mitochondrial haplotype carried by interacting pairs of larvae
 affects survival to adulthood, as well as the fitness of the adults.
 Although mtDNA had no detectable direct or indirect genetic effect on
 larva-to-adult survival, the fitness of male and female adults was
 significantly affected by their own mtDNA and the mtDNA carried by their
 social partner in the larval stage. Thus, mtDNA mutations that alter the
 effect of male larvae on nearby female larvae (which often carry the same
 mutation, due to kinship) could theoretically respond to kin selection. We
 discuss the implications of our findings for the evolution of mitochondria
 and other maternally inherited endosymbionts.
description: This data was collected during laboratory experiments using
 Drosophila melanogaster. It has been used in the manuscript titled
 "Sibling rivalry vs mother’s curse: can kin competition facilitate a
 response to selection on male mitochondria?", to be published in
 <em>Proceedings of the Royal Society B</em>.
DOI: 10.5061/dryad.44j0zpcb9
title: Data from: Contrasting global patterns of spatially periodic fairy circles and regular insect nests in drylands

description: Numerical analysis of spatial pattern is widely used in ecology to
 describe the characteristics of floral and faunal distributions. These
 methods allow attribution of pattern to causal mechanisms by uncovering
 the specific signatures of patterns and causal agents. For example,
 grassland‐gap patterns called fairy circles (FCs) in Namibia and Australia
 are characterized by highly regular and homogenous distributions across
 landscapes that show spatially periodic ordering. These FCs have been
 suggested to be caused by both social insects and competitive plant
 interactions. We compared eight Namibian and Australian FC patterns and
 also modeled FCs to 16 patterns of social insect nests in Africa,
 Australia, and America that include the most regular termite mound
 patterns known. For pattern‐process inference, we used spatial statistics
 based on both nearest‐neighbor analysis and neighborhood‐density
 functions. None of the analyzed insect‐nest distributions attain the
 spatially periodic ordering that is typical of FCs. The inherently more
 variable patterns of termite and ant nests are commonly attributable to
 well documented aspects of the faunal life‐history. Our quantitative
 evidence from drylands shows that the more variable insect‐nest
 distributions in water‐limited environments cannot explain the
 characteristic spatial signature of FCs. The analysis demonstrates the
 interpretation of scale‐dependent neighborhood‐density functions and that
 it is the identification of unique spatial signatures in regular patterns
 that need to be linked to process. While our results cannot verify a
 specific hypothesis, they support the hypothesis that FCs in these
 drylands are more likely an emergent vegetation pattern caused by strong
 plant competition for water.
DOI: 10.5061/dryad.g1jwstqnp
title: Community-level reorganizations following migratory pollinator dynamics along a latitudinal gradient

description: Predicting how communities re-arrange in response to changes in species
 composition remains a key challenge in ecology. Migratory species, which
 enter and leave communities across latitudinal gradients, offer us a
 unique opportunity to evaluate community and species-level responses to a
 shift in community composition. We focused on a migratory hummingbird and
 the communities that host it along a latitudinal and species diversity
 gradient. Our results show higher niche overlap in more diverse
 communities, allowing resident species to compensate for the loss of the
 migrant in providing pollination services. Contrastingly, in less diverse
 communities, the migrant behaves as a specialist, monopolizing abundant
 resources. In its absence, its role is not fully covered by resident
 species, resulting in a decrease in the fruit set of the migrant´s
 preferred plant species. These results help us understand the potential
 impacts of biodiversity loss and have important implications for community
 persistence given expected changes in the migratory behaviors of some
 species.
description: This dataset includes observed feeding interactions between
 hummingbirds and plants at three localities along the migratory route of
 the hummingbird Selasphorus rufus, Mexico, California and Alaska. Data are
 used to create quantitative matrices of interaction frequencies and
 analyed using GLMMs to evaluate the influence of the presence of the
 migratory species on community structure and ecosystem
 functioning.
DOI: 10.5061/dryad.cvdncjt1n
title: The origins of coca: museum genomics reveals multiple independent domestications from progenitor Erythroxylum gracilipes

description: Coca is the natural source of cocaine as well as a sacred and medicinal
 plant farmed by South American Amerindians and mestizos. The coca crop
 comprises four closely related varieties classified into two species
 (Amazonian and Huánuco varieties within Erythroxylum coca Lam., and
 Colombian and Trujillo varieties within E. novogranatense (D.Morris)
 Hieron.) but our understanding of their wild progenitor(s) and origins
 remains rudimentary. In this study we use genomic data from natural
 history collections to estimate the geographic origins and genetic
 diversity of this economically and culturally important crop in the
 context of its wild relatives. Our phylogeographic analyses clearly
 demonstrate the four varieties of coca comprise two or three exclusive
 groups nested within the diverse lineages of the widespread, wild species
 E. gracilipes; establishing a new and robust hypothesis of domestication
 wherein coca originated two or three times from this wild progenitor. The
 Colombian and Trujillo coca varieties are descended from a single, ancient
 domestication event in northwestern South America. Huánuco coca was
 domesticated more recently, possibly in southeastern Peru. Amazonian coca
 either shares a common domesticated ancestor with Huánuco coca, or it was
 the product of a third and most recent independent domestication event in
 the western Amazon basin. This chronology of coca domestication reveals
 different Holocene peoples in South America were able to independently
 transform the same natural resource to serve their needs; in this case, a
 workaday stimulant.
description: Hybridization-based exon capture using custom probes (White et
 al. 2019, <em>American Journal of Botany</em>).
description: Raw data are on Genbank's SRA database.
DOI: 10.5061/dryad.tqjq2bvw5
title: Data from: Adaptive genetic potential and plasticity of trait variation in the foundation prairie grass Andropogon gerardii across the US Great Plains’ climate gradient: Implications for climate change and restoration

description: Plant response to climate depends on a species’ adaptive potential. To
 address this, we used reciprocal gardens to detect genetic and
 environmental plasticity effects on phenotypic variation and combined with
 genetic analyses. Four reciprocal garden sites were planted with three
 regional ecotypes of Andropogon gerardii, a dominant Great Plains prairie
 grass, using dry, mesic, wet ecotypes originating from western KS to
 Illinois that span 500 to 1,200 mm rainfall year-1. We aimed to answer:
 (1) What is the relative role of genetic constraints and phenotypic
 plasticity in controlling phenotypes? 2) When planted in the home site, is
 there a trait syndrome for each ecotype? 3) How are genotypes and
 phenotypes structured by climate? (4) What are implications of these
 results for response to climate change and use of ecotypes for
 restoration? Surprisingly, we did not detect consistent local adaptation.
 Rather, we detected co-gradient variation primarily for most vegetative
 responses. All ecotypes were stunted in western KS. Eastward, the wet
 ecotype was increasingly robust relative to other ecotypes. In contrast,
 fitness showed evidence for local adaptation in wet and dry ecotypes with
 wet and mesic ecotypes producing little seed in western KS. Earlier
 flowering time in the dry ecotype suggests adaptation to end of season
 drought. Considering ecotype traits in home site, the dry ecotype was
 characterized by reduced canopy area and diameter, short plants, and low
 vegetative biomass and putatively adapted to water limitation. The wet
 ecotype was robust, tall with high biomass and wide leaves putatively
 adapted for the highly competitive, light-limited Eastern Great Plains.
 Ecotype differentiation was supported by random forest classification and
 PCA. We detected genetic differentiation and outlier genes associated
 primarily with precipitation. We identified candidate gene GA1 for which
 allele frequency associated with plant height. Sourcing of climate adapted
 ecotypes should be considered for restoration.
DOI: 10.5061/dryad.t1g1jwt05
title: Data from: Accumulation curves of environmental DNA sequences predict coastal fish diversity in the Coral Triangle

description: Environmental DNA (eDNA) has the potential to provide more comprehensive
 biodiversity assessments particularly for vertebrates in species-rich
 regions. Yet, this method requires the completeness of a reference
 database, i.e. a list of DNA sequences attached to each species, which is
 never met. As an alternative, a diversity of Operational Taxonomic Units
 (OTUs) can be extracted from eDNA metabarcoding. However, the extent to
 which the diversity of OTUs provided by a limited eDNA sampling effort can
 predict regional species diversity is unknown. Here, by modelling OTU
 accumulation curves of eDNA seawater samples across the Coral Triangle, we
 obtained an asymptote reaching 1,531 fish OTUs while 1,611 fish species
 are recorded in the region. Besides, we also accurately predict (R² =
 0.92) the distribution of species richness among fish families from
 OTU-based asymptotes. Thus, the multi-model framework of OTU accumulation
 curves extends the use of eDNA metabarcoding in ecology, biogeography and
 conservation.
description: Environmental DNA (eDNA) was extracted from 2L seawater samples as described in the file <i>Methods </i>section of the paper. Retrieved eDNA was then amplified using a teleost-specific 12S mitochondrial rDNA primer (teleo), sequenced and processed using two bioinformatics pipelines. The files obitools_lengguru.csv and swarm_lengguru.csv are the outputs of the OBITools and SWARM pipeline, respectively. It represents the raw data merged with metadata and linking the occurence tables with taxonomical assignments, prior to quality filtering.   
description: <b>The bioinformatic
 pipelines scripts used to generate both datasets are available in Gitlab
 following the links below :</b> https://gitlab.mbb.univ-montp2.fr/edna/snakemake_only_obitools https://gitlab.mbb.univ-montp2.fr/edna/bash_swarm
DOI: 10.5061/dryad.ffbg79crg
title: Evolution of body size and wing shape trade-offs in arsenurine silkmoths

description: One of the key objectives in biological research is understanding how
 evolutionary processes have produced Earth's diversity. A critical
 step towards revealing these processes is an investigation of evolutionary
 tradeoffs – that is, the opposing pressures of multiple selective forces.
 For millennia, nocturnal moths have had to balance successful flight, as
 they search for mates or host plants, with evading bat predators. However,
 the potential for evolutionary trade-offs between wing shape and body size
 are poorly understood. In this study, we used phylogenomics and geometric
 morphometrics to examine the evolution of wing shape in the wild silkmoth
 subfamily Arsenurinae (Saturniidae) and evaluate potential evolutionary
 relationships between body size and wing shape. The phylogeny was inferred
 based on 782 loci from target capture data of 42 arsenurine species
 representing all 10 recognized genera. After detecting in our data one of
 the most vexing problems in phylogenetic inference – a region of a tree
 that possesses short branches and no “support” for relationships (i.e., a
 polytomy), we looked for hidden phylogenomic signal (i.e., inspecting
 differing phylogenetic inferences, alternative support values, quartets,
 and phylogenetic networks) to better illuminate the most probable generic
 relationships within the subfamily. We found there are putative
 evolutionary trade-offs between wing shape, body size, and the interaction
 of fore- and hindwing shape. Namely, body size tends to decrease with
 increasing hindwing length but increases as forewing shape becomes more
 complex. Additionally, the type of hindwing (i.e., tail or no tail) a
 lineage possesses has a significant effect on the complexity of forewing
 shape. We outline possible selective forces driving the complex hindwing
 shapes that make Arsenurinae, and silkmoths as a whole, so charismatic.
description: 1. Anchored Hybrid Enrichment phylogenomics (includes all
 consensus alignment FASTA files, loci information, partition files, tree
 files, and other essential data files used for phylogenetic
 inference) 2. Wing shape data for geometric
 morphometrics and elliptical fourier analysis (includes all images for
 geometric morphometrics and outputs for comparative analyses)
DOI: 10.5061/dryad.q2bvq83g9
title: Data from: Molecular evolutionary analysis of nematode Zona Pellucida (ZP) modules reveals disulfide-bond reshuffling and standalone ZP-C domains

description: Zona pellucida (ZP) modules mediate extracellular protein-protein
 interactions and contribute to important biological processes including
 syngamy and cellular morphogenesis. While some biomedically-relevant ZP
 modules are well-studied, little is known about the protein family’s
 broad-scale diversity and evolution. The increasing availability of
 sequenced genomes from “non-model” systems provides a valuable opportunity
 to address this issue, and to use comparative approaches to gain new
 insights into ZP module biology. Here, through phylogenetic and structural
 exploration of ZP module diversity across the nematode phylum, I report
 evidence that speaks to two important aspects of ZP module biology. First,
 I show that ZP-C domains—which in some modules act as regulators of ZP-N
 domain-mediated polymerization activity, and which have never before been
 found in isolation—can indeed be found as standalone domains. These
 standalone ZP-C domain proteins originated in independent (paralogous)
 lineages prior to the diversification of extant nematodes, after which
 they evolved under strong stabilizing selection, suggesting the presence
 of ZP-N domain-independent functionality. Second, I provide a much-needed
 phylogenetic perspective on disulfide bond variability, uncovering
 evidence for both convergent evolution and disulfide-bond reshuffling.
 This result has implications for our evolutionary understanding and
 classification of ZP module structural diversity and highlights the
 usefulness of phylogenetics and diverse sampling for protein structural
 biology. All told, these findings set the stage for broad-scale
 (cross-phyla) evolutionary analysis of ZP modules and position
 Caenorhabditis elegans and other nematodes as important experimental
 systems for exploring the evolution of ZP modules and their constituent
 domains.
DOI: 10.5061/dryad.ghx3ffbkg
title: Moose (Alces alces) parturition dates, Sweden

description: In northern environments, the period of access to high-quality forage is
 limited, exerting strong selective pressure to optimize the timing of
 parturition. We analysed timing and variation in moose parturition dates
 of 555 females at 18 study sites across 12ᵒ of latitude (56-68ᵒ N, 1,350
 km) in Sweden. We found evidence for a spatial match of parturition timing
 to vegetation onset, but no evidence that moose adjust parturition to
 vegetation onset in a given year. We found a breakpoint at 64ᵒ N. Despite
 adaptation across latitudes, temporal divergences occurred. Females
 &lt;64 ᵒN calved after vegetation onset and females &gt;64 ᵒN
 calved before. Here, parturition before vegetation onset might be a
 strategy to optimize forage utilization time with the very short growing
 season. Highly seasonal environments such as at higher latitudes may make
 it advantageous to adapt parturition towards long-term climatic patterns
 by matching the most favourable period. Given the direction of temporal
 divergence, our study suggests that climate change may have less of an
 impact on moose parturition at northern latitudes than southern latitudes.
description: Includes data on moose calving dates across 12 degrees of
 latitude in Sweden. More details on data collection and methods can be
 found in the main doucment and supplementary material of the published
 article (RSBL-2020-0044, Biology Letters).
DOI: 10.5061/dryad.0rxwdbrww
title: Data from: Early Miocene marine ostracods from southwestern India: implications for their biogeography and the closure of the Tethyan Seaway

description: Twenty-six genera and 34 species of early Miocene Indian shallow-marine
 ostracods were examined for taxonomy and paleobiogeography. A new genus
 Paractinocythereis and new species Costa ponticulocarinata were described.
 Early Miocene Indian ostracod fauna shows strong affinity to
 Eocene–Miocene Eastern and Western Tethyan ostracod faunas and
 Miocene–Recent Indo-Pacific ostracod fauna, supporting the Hopping Hotspot
 Hypothesis that Tethyan biodiversity hotspot have shifted eastward through
 Arabia to Indo-Australian Archipelago (IAA) together with concomitant
 biogeographic shifts of the Tethyan elements. The result also indicated an
 inverse westward distributional shift in a genus. It is important to note
 that Paleogene and Miocene shallow-marine ostracods from the IAA region
 remain poorly investigated, and more fossil ostracod data is needed to
 better test the Hopping Hotspot Hypothesis.
description: High-resolution figures of ostracod SEM images (Figs 2–19).
DOI: 10.5061/dryad.2ngf1vhk9
title: Data from: Genetic evidence for sexual reproduction and multiple infections of Norway spruce cones by the rust fungus Thekopsora areolata

description: Rust fungi are obligate parasites of plants with complex and in many cases
 poorly known life cycles which may include host alteration and up to five
 spore types with haploid, diploid and dikaryotic nuclear stages. This
 study supports that Thekopasora areolata, the causal agent of
 cherry-spruce rust in Norway spruce, is a macrocyclic heteroecious fungus
 with all five spore stages which uses two host plants Prunus padus and
 Picea abies to complete its life cycle. High genotypic diversity without
 population structure was found, which suggests predominantly sexual
 reproduction, random mating and a high gene flow within and between the
 populations in Fennoscandia. There was no evidence for an autoecious life
 cycle resulting from aeciospore infection of pistillate cones that would
 explain the previously reported rust epidemics without the alternate host.
 However, within cones and scales identical multilocus genotypes were
 repeatedly sampled which can be explained by vegetative growth of the
 fertilised mycelia or repeated mating of mycelium by spermatia of the same
 genotype. The high genotypic diversity within cones and haplotype
 inference show that each pistillate cone is infected by several
 basidiospores. This study provides genetic evidence for high gene flow,
 sexual reproduction and multiple infections of Norway spruce cone by the
 rust fungus T. areolata which expands the general understanding of the
 biology of rust fungi.
description: <i>Partially nested hierarchical
 sampling</i> Location
 level:<i> Picea abies </i>cones with aecia were
 collected from 7 different locations in Sweden, Norway, and Finland. At
 each location 30 cones were collected, from which one scale with aecia per
 cone and one aecium per scale were randomly sampled. At tree
 level: a more extensive sampling was made at the seed orchard in
 Ålbrunna (Sweden), where 100 cones with aecia were sampled from 6
 different trees at a distance of ca. 20 m to 600 m from each other. From
 each cone, one scale with aecia and one aecium per scale were randomly
 sampled. At cone level: 10 cones with aecia were
 randomly sampled from two locations in Sweden (a-1 and a-4) and split
 longitudinally to select 10 scales across each cone, from which 10 aecia
 per scale were randomly sampled (100 aecia per cone). At scale
 level: 3 individual scales with aecia from cones from two
 different locations in Sweden (a-1 and a-4) were thoroughly sampled (ca.
 40 aecia per scale). <i>Single aecium
 genotyping</i> DNA was extracted from each
 aecium following the protocol of Capador et al., (2018). The samples were
 genotyped with 8 polymorphic microsatellites markers; Tha9, Tha61, Tha91,
 Tha92, Tha96, Tha105, Tha136, and Tha137, microsatellite amplification and
 scoring was performed as formerly described (Capador et al., 2018) except
 for a subset of samples which were analysed with DreamTaq (ThermoFisher)
 instead of PIR00 (Sigma).
description: The dataset is in Genalex format
DOI: 10.5061/dryad.931zcrjh2
title: Growth of carbon nanofibres on molybdenum carbide nanowires and their self-decoration with noble-metal nanoparticles

description: High specific surface area makes carbon nanofibres suitable for catalyst
 support. Here we report on optimisation of carbon nanofibre (CNF) growth
 on molybdenum carbide nanowires (MoCNW) by direct carburization of Mo6S2I8
 nanowire bundles. Typical CNFs obtained by this method are several
 hundreds of nanometres long at a diameter of 10-20 nm. We show that
 nanofibre growth does not depend on the initial morphology of the
 nanowires: nanofibres grow on individual bundles of MoCNW, on dense
 networks of nanowires deposited on silicon substrate, and on free-standing
 nanowire foils. We find that carbon nanofibres remain firmly attached to
 the nanowires even if they are modified into Mo2C and further into MoS2
 nanowires. The method thus enables production of a novel hybrid material
 composed of MoS2 nanowires densely covered with carbon nanofibres. We have
 additionally shown that the obtained CNFs can easily be self-decorated
 with platinum nanoparticles with diameters of several nanometres directly
 from water solution at room temperature without reducing agents. Such
 efficient synthesis and decoration process yield hybrid
 platinum/CNF/molybdenum-based NW materials, which are a promising material
 for a wide range of possible future applications, including sensitive
 sensorics and improved catalysis.
description: X-ray powder diffraction (XRD) was performed at room temperature
 using Bruker AXS D4 Endeavor diffractometer with Cu-Ka radiation and Sol-X
 energy-dispersive detector within angular range 2Θ from
 10<sup>o</sup> to 70<sup>o</sup> with a step size
 of 0.02<sup>o</sup> and a collection time of 2 s at a rotation
 of 6 rpm. EDS spectrum was obtained by high-resolution
 transmission electron microscope (Jeol JEM-2100F, 200 keV), allowing high
 contrast imaging and simultaneous EDS.