cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b1qd22n
title: Data from: Fitness of reciprocal F1 hybrids between Rhinanthus minor and Rhinanthus major under controlled conditions and in the field

description: The performance of first‐generation hybrids determines to a large extent
 the long‐term outcome of hybridization in natural populations. F1 hybrids
 can facilitate further gene flow between the two parental species,
 especially in animal‐pollinated flowering plants. We studied the
 performance of reciprocal F1 hybrids between Rhinanthus minor and R.
 major, two hemiparasitic, annual, self‐compatible plant species, from seed
 germination to seed production under controlled conditions and in the
 field. We sowed seeds with known ancestry outdoors before winter and
 followed the complete life cycle until plant death in July the following
 season. Germination under laboratory conditions was much lower for the F1
 hybrid formed on R. major compared to the reciprocal hybrid formed on R.
 minor, and this confirmed previous results from similar experiments.
 However, this difference was not found under field conditions, which seems
 to indicate that the experimental conditions used for germination in the
 lab are not representative for the germination behaviour of the hybrids
 under more natural conditions. The earlier interpretation that F1 hybrid
 seeds formed on R. major face intrinsic genetic incompatibilities
 therefore appears to be incorrect. Both F1 hybrids performed as well as or
 sometimes better than R. minor, which had a higher fitness than R. major
 in one of the two years in the greenhouse and in the field transplant
 experiment. The high fitness of the F1 hybrids confirm findings from
 naturally mixed populations, where F1 hybrids appear in the first year
 after the two species meet and which leads to extensive advanced‐hybrid
 formation and introgression in subsequent generations.
description: Wesselingh_2019_Rhinanthus_germination_labresults of germination trial in laboratoryWesselingh_2019_Rhinanthus_hybrids_field_emergence_survivalresults of field transplant experiment: emergence of seedlings and survival until floweringWesselingh_2019_Rhinanthus_hybrids_field_flowers_seedsfield transplant: flower and seed production of surviving plantsWesselingh_2019_Rhinanthus_hybrids_greenhouse_flowersflower production of plants in the greenhouse in 2013Wesselingh_2019_Rhinanthus_hybrids_greenhouse_2013_flowers.csvWesselingh_2019_Rhinanthus_hybrids_greenhouse_2014_flowersflower production by plants in the greenhouse in 2014
DOI: 10.5281/zenodo.18391732
title: Dataset
DOI: 10.5281/zenodo.18391731
title: Dataset
DOI: 10.5061/dryad.rh2dq7j
title: Data from: Ecological speciation in sympatric palms: 3. genetic map reveals genomic islands underlying species divergence in Howea

description: Although it is now widely accepted that speciation can occur in the face
 of continuous gene flow, with little or no spatial separation, the
 mechanisms and genomic architectures that permit such divergence are still
 debated. Here, we examined speciation in the face of gene flow in the
 Howea palms of Lord Howe Island, Australia. We built a genetic map using a
 novel method applicable to long-lived tree species, combining it with
 double digest restriction-site associated DNA sequencing of multiple
 individuals. Based upon various metrics, we detected 46 highly
 differentiated regions throughout the genome, some of which contained
 genes with functions that are particularly relevant to the speciation
 scenario for Howea, specifically salt and drought tolerance.
description: process_raw_data_to_mapCollection of scripts to process reads for the linkage mapping panel and assign genotypes in genepop format for linkage map constructionLinkage map marker positionsMarker positions on Linkage groups in cMmap_sequencesConsensus sequences for markers included in linkage map.Outlier_analysisR script to perform outlier analyses
DOI: 10.5061/dryad.4dq31c5
title: Data from: Trophic position of consumers and size structure of food webs across aquatic and terrestrial ecosystems

description: Do large organisms occupy higher trophic levels? Predators are often
 larger than their prey in food chains, but empirical evidence for positive
 body mass - trophic level scaling for entire food webs mostly comes from
 marine communities based on unicellular producers. Using published data on
 stable isotope compositions of 1093 consumer species, we explored how
 trophic level scales with body size, food-web type (green vs. brown) and
 phylogenetic group across biomes. In contrast to widespread assumptions,
 the relationship of body size on trophic level of consumers, from protists
 to large vertebrates, was not significant per se, but varied among
 ecosystem types and animal groups. The correlation between body size and
 trophic level was strong in marine, weak in freshwater and absent in
 terrestrial consumers, which was observed also at the scale of local food
 webs. Vertebrates occupied higher trophic positions than invertebrates and
 green trophic chains were longer than brown in aquatic (primarily marine),
 but not in terrestrial food webs. Variations in body size of the top
 predators suggest that terrestrial and many freshwater food webs are
 size-compartmentalized, implying different trophic dynamics and responses
 to perturbations than in size-structured marine food webs..
description: PotapovST1Stable isotope data compiled from the published literature.PotapovST2Classification and body sizes of species.PotapovST5Selected food webs for analysis.
DOI: 10.5061/dryad.76t6j77
title: Data from: Managing the risk of genetic swamping of a rare and restricted tree

description: Hybridisation is a complex process that has important evolutionary
 consequences. In the case of rare species, a comprehensive understanding
 of inter-specific hybridisation can be critical for their conservation and
 management. Eucalyptus tetrapleura is a rare species of ironbark that is
 restricted to a 40 km × 100 km area around Grafton on the North Coast of
 New South Wales (Australia), and is distinctive in that it has four ribs
 on the sides of its buds and fruits. In recent years, central populations
 of E. tetrapleura have been cleared to facilitate upgrades to one of the
 major highways in eastern Australia. This has led to increased habitat
 fragmentation, and there are now concerns that the species is at risk of
 genetic swamping by more common ironbark relatives. In this study, we
 investigated the population genetics and patterns of gene flow in E.
 tetrapleura. We used DArTseq to genotype samples collected from across the
 known distribution of E. tetrapleura, as well as leaf material collected
 from co-occurring ironbark species. We found that while E. tetrapleura was
 a distinct evolutionary lineage, there was evidence of gene flow between
 this species and other ironbarks. Furthermore, many populations that had
 been identified as E. tetrapleura on the basis of morphology were of
 hybrid origin, thus the range of the species was much smaller than
 previously thought. Overall, our findings demonstrate how genomic methods
 can improve our understanding of admixture across closely related
 lineages, which can be used to inform the restoration of rare species.
description: Eucalyptus tetrapleura
 _DArTseq_Report_DE16-2415_raw data
DOI: 10.5061/dryad.p1255b3
title: Data from: Landscape structure mediates zoochorous-dispersed seed rain under isolated pasture trees across distinct tropical regions

description: Context: Isolated pasture trees play an important role in forest recovery
 within fragmented tropical landscapes by attracting seed dispersers and
 facilitating seedling growth. However, studies with conflicting results
 have led to confusion about what drives variation in zoochorous-dispersed
 seed rain patterns under isolated tree canopies. Objectives: To assess the
 role of landscape and biological factors impacting zoochorous-dispersed
 seed rain under isolated pasture trees across three tropical regions of
 the world. Methods: We measured seed dispersal under 144 isolated pasture
 trees found in 12 fragmented tropical and sub-tropical landscapes in
 Australia, Colombia and Nigeria. Using linear mixed effect models, we
 modeled seed diversity, abundance, richness and evenness as functions of
 the biological features and landscape context of isolated trees. Results:
 Throughout all regions, the amount of woody vegetation surrounding trees
 in pastures was negatively related to rainforest seed diversity, evenness
 and abundance. Seed diversity and evenness increased significantly with
 the distance of isolated trees to forest fragments in the Australian
 sub-tropics, but elsewhere, seed diversity and evenness tended to decline
 with distance to forest, though not significantly. Conclusions: Our
 results suggest that the tree composition of landscapes surrounding
 isolated pasture trees is important for influencing zoochorous-dispersed
 seed rain, regardless of the region studied. Our study highlights the
 prominent role of landscape-scale, rather than local-scale factors on seed
 dispersal to isolated pasture trees, while providing strong evidence that
 early stage successional processes involving isolated pasture trees are
 similar throughout global tropical regions.
description: Charles
 _el_al_dataThis is an Excel file
 containing two worksheets. The first (Location_and_seed_data) contains all
 data on the locations of each isolated tree used in this study and the
 diversity of seeds collected under them as well as in control plots. The
 second sheet (seasonal_data) gives data on seed diversity under each
 isolated tree broken down by the season in which seeds were
 collected.Charles_et_al_data.xlsx
DOI: 10.5061/dryad.k02pq01
title: Larger genomes linked to slower development and loss of late-developing traits

description: Genome size varies widely among organisms and is known to affect
 vertebrate development, morphology, and physiology. In amphibians, genome
 size is hypothesized to contribute to loss of late-forming structures,
 although this hypothesis has mainly been discussed in salamanders. Here we
 estimated genome size for 22 anuran species and combined this novel
 dataset with existing genome size data for an additional 234 anuran
 species to determine whether larger genome size is associated with loss of
 a late-forming anuran sensory structure, the tympanic middle ear. We
 established that genome size is negatively correlated with development
 rate across 90 anuran species and found that genome size evolution is
 correlated with evolutionary loss of the middle ear bone (columella) among
 241 species (224 eared and 17 earless). We further tested whether the
 development of the tympanic middle ear could be constrained by large cell
 sizes and small body sizes during key stages of tympanic middle ear
 development (metamorphosis). Together, our evidence suggests that larger
 genomes, slower development rate, and smaller body sizes at metamorphosis
 may contribute to the loss of the anuran tympanic middle ear. We conclude
 that increases in anuran genome size, although less drastic than in
 salamanders, may affect development of late-forming traits.
description: Womack_etal_2019_GenomeSizeDataTable_ForDryadData used and relevant references for Womack et al. 2019 publication in American Naturalist.GenomeSizeDataTable_ForDryad.csv
DOI: 10.5061/dryad.n6n6495
title: Data from: Tail loss and telomeres: consequences of large-scale tissue regeneration in a terrestrial ectotherm.

description: Large-scale tissue regeneration has potential consequences for telomere
 length through increases in cell division and changes in metabolism which
 increase the potential for oxidative stress damage to telomeres. The
 effects of regeneration on telomere dynamics have been studied in fish and
 marine invertebrates, but the literature is scarce for terrestrial
 species. We experimentally induced tail autotomy in a lizard (Niveoscincus
 ocellatus) and assessed relative telomere length (RTL) in blood samples
 before and after partial tail regeneration while concurrently measuring
 reactive oxygen species (ROS) levels. The change in ROS levels was a
 significant explanatory variable for the change in RTL over the sixty-day
 experiment. At the average value of ROS change, the mean RTL increased
 significantly in the control group (intact tails), but there was no such
 evidence in the regenerating group. In contrast, ROS levels decreased
 significantly in the regenerating group, but there was no such evidence in
 the control group. Combined, these results suggest that tail regeneration
 following autotomy involves a response to oxidative stress and this
 potentially comes at a cost to telomere repair. This change in telomere
 maintenance demonstrates a potential long-term cost of tail regeneration
 beyond the re-growth of tissue itself.
description: Fitzpatrick et al
 data
DOI: 10.5061/dryad.1rj6442
title: Data from: A genome-wide investigation of the worldwide invader Sargassum muticum shows high success albeit (almost) no genetic diversity

description: Twenty-years of genetic studies of marine invaders have shown that
 successful invaders are often characterized by native and introduced
 populations displaying similar levels of genetic diversity. This pattern
 is presumably due to high propagule pressure and repeated introductions.
 The opposite pattern is reported in this study of the brown seaweed,
 Sargassum muticum, an emblematic species for circumglobal invasions.
 Albeit demonstrating polymorphism in the native range, microsatellites
 failed to detect any genetic variation over 1269 individuals sampled from
 46 locations over the Pacific-Atlantic introduction range.
 Single-Nucleotide Polymorphisms (SNPs) obtained from ddRAD-sequencing
 revealed some genetic variation, but confirmed severe founder events in
 both the Pacific and Atlantic introduction ranges. Our study thus
 exemplifies the need for extreme caution in interpreting neutral genetic
 diversity as a proxy for invasive potential. Our results confirm a
 previously hypothesized trans-oceanic secondary introduction from NE
 Pacific to Europe. However, the SNPs panel unexpectedly revealed two
 additional distinct genetic origins of introductions. Also, conversely to
 scenarios based on historical records, southern rather than northern NE
 Pacific populations could have seeded most of the European populations.
 Finally, the most recently introduced populations showed the lowest
 selfing rates, suggesting higher levels of recombination might be
 beneficial at the early stage of the introduction process (i.e.,
 facilitating evolutionary novelties), whereas uniparental reproduction
 might be favored later in sustainably established populations (i.e.,
 sustaining local adaptation).
description: Microsatellite
 datasetMicrosatellite dataset
 including genotype at each of the 14 study loci and multilocus genotype
 (MLG) with their code as used in Fig. 1 of the associated paper. Sampling
 information (populations code, collectors, sampling year, number of
 individuals genotyped with microsatellite markers) are detailed in Table
 S1 of the associated paper.LeCam et
 al._Sargassum_Data&Microsatellite.xlsxRADseq VCF file (Sargassum muticum)VCF file with ddRad-seq dataset. This dataset comprises 8788 polymorphic loci in a sample of 300 individuals from 21 sampling sites. Raw data had been filtered to keep loci genotyped in minimum 80% of the populations and 50% of individuals per population, representing 20% missing data across the whole dataset. Individual codes are described in the associated microsatellite dataset (see Excell file) and Table S1 of the associated paper.LeCam_Sargassum_RADSeq.vcf
DOI: 10.5061/dryad.5ck2qs1
title: Data from: The functional trait space of tree species is influenced by the species richness of the canopy and the type of forest

description: Analysing how species modify their trait expression along a diversity
 gradient brings insight about the role that intraspecific variability
 plays over species interactions, e.g. competition versus complementarity.
 Here, we evaluated the functional trait space of nine tree species
 dominant in three types of European forests (a continental-Mediterranean,
 a mountainous mixed temperate and a boreal) growing in communities with
 different species richness in the canopy, including pure stands. We
 compiled whole-plant and leaf traits in 1719 individuals, and used them to
 quantify species trait hypervolumes in communities with different tree
 species richness. We investigated changes along the species richness
 gradient to disentangle species responses to the neighbouring environment,
 in terms of hypervolume size (trait variance), shape (trait relative
 importance) and centroid translation (shifts of mean trait values) using
 null models. Our main results showed differences in trait variance and
 shifts of mean values along the tree diversity gradient, with shorter
 trees but with larger crowns in mixed stands. We found constrained
 functional spaces (trait convergence) in pure stands, suggesting an
 important intraspecific competition, and expanded functional spaces (trait
 divergence) in two-species admixtures, suggesting competition release due
 to interspecific complementarity. Nevertheless, further responses to
 increasing species richness were different for each forest type, waning
 species complementarity in sites with limiting conditions for growth. Our
 results demonstrate that tree species phenotypes respond to the species
 richness in the canopy in European forests, boosting species
 complementarity at low level of canopy diversity and with a site-specific
 pattern at greater level of species richness. These outcomes evidence the
 limitation of functional diversity measures based only on traits from pure
 stands or general trait database values.
description: trait data of European
 tree species along a species richness gradient in the
 canopyit includes trait data
 measured in 1,719 trees belonging to 9 tree species growing in three types
 of forests in Europe (a boreal, a temperate and a Mediterranean). Surveyed
 individuals of each species were in stands with different species richness
 in the canopy going from monocultures to mixed stands with 3 and 4
 species.data_base.xlsx
DOI: 10.15468/p9ybag
title: Academy of Natural Sciences of Drexel University
DOI: 10.15468/njgg1a
title: Brown University Herbarium - Fungi

description: The Brown University Herbarium was founded in 1869 when the University acquired the collections of the Providence Franklin Society and Stephen Thayer Olney. The collection includes around 100,000 plant specimens and is an important depository of Rhode Island and New England collections. It is also rich in western and southern North American plants and includes special sets of historically valuable specimens from 19th and early 20th century western US expeditions. Among other important collections, the herbarium also includes a full set of Charles Wright&rsquo;s Cuban plants (1856-1867) and a unique and classic collection of Carex.
DOI: 10.5061/dryad.8cj221n
title: Data from: Rapid, complete reproductive isolation in two closely-related Zosterops White-eye bird species despite broadly overlapping ranges

description: Examining what happens when two closely-related species come into
 secondary contact provides insight into the later stages of the speciation
 process. The Zosteropidae family of birds is one of the most rapidly
 speciating vertebrate lineages. Members of this family are highly vagile
 and geographically widespread, raising the question of how divergence can
 occur if populations can easily come into secondary contact. On the small
 island of Kolombangara, two closely-related non-sister species of
 White-eyes, Zosterops kulambangrae and Z. murphyi, are distributed along
 an elevational gradient and come into secondary contact at mid-elevations.
 We captured 134 individuals of both species along two elevational
 transects. Using genotyping-by-sequencing data and a mitochondrial marker,
 we found no evidence of past hybridization events and strong persistence
 of species boundaries, even though the species have only been diverging
 for approximately two million years. We explore potential reproductive
 barriers that allow the two species to coexist in sympatry, including
 premating isolation based on divergence in plumage and song. We also
 conducted a literature review to determine the time it takes to evolve
 complete reproductive isolation in congeneric avian species/subspecies in
 secondary contact (restricted to cases where congeneric taxa are
 parapatric or have a hybrid zone), finding our study is one of the
 youngest examples of complete reproductive isolation studied in a genomic
 context reported in birds.
description: Kolombangara Zosterops
 Genomic SNP fileThis vcf file contains
 86,432 SNPs from GBS sequencing of genetic samples from 76 Zosterops
 kulambangrae and 58 Z. murphyi.Kolo_SNPs_86432.vcfZosterops ND2 Mitochondrial Gene 744bpThis file contains sequences of the mtDNA gene ND2 for 75 Zosterops kulambangrae and 56 Z. murphyi. Each sequence is 744bp in length.Zosterops_ND2_744bp.NEXBody Patch Color Spectral DataThis zip file contains all of the raw spectral files (in the Master.Transmission format) from the back, belly, chest, and rump patches on each captured bird (Zosterops kulambangrae and Z. murphyi). A set of 3-4 feathers was taken from each body patch and mounted on black paper. We used an Ocean Optics USB2000 Spectrophotometer connected to a pulsed Xenon PX-2 light source.Call FilesThis zip file contains the raw sound .wav files from 4 individual/group recordings of each species.Call_files.zipSong FilesThis zip file contains the raw sound .wav files from 8 Zosterops kulambangrae and 3 Z. murphyi recordings.Song_files.zip
DOI: 10.5061/dryad.db660b8
title: Data from: Multi-species comparisons of snakes identify coordinated signaling networks underlying post-feeding intestinal regeneration

description: Several snake species that feed infrequently in nature have evolved the
 ability to massively upregulate intestinal form and function with each
 meal. While fasting, these snakes downregulate intestinal form and
 function and upon feeding restore intestinal structure and function
 through major increases in cell growth and proliferation, metabolism, and
 upregulation of digestive function. Previous studies have identified
 changes in gene expression that underlie this regenerative growth of the
 python intestine, but the unique features that differentiate this extreme
 regenerative growth from non-regenerative post-feeding responses exhibited
 by snakes that feed more frequently remain unclear. Here, we leveraged
 variation in regenerative capacity across three snake species – two
 distantly-related lineages (Crotalus and Python) that experience
 regenerative growth, and one (Nerodia) that does not – to infer molecular
 mechanisms underlying intestinal regeneration using transcriptomic and
 proteomic approaches. Utilizing a comparative approach, we identify a
 suite of growth, stress response, and DNA damage response signaling
 pathways with inferred activity specifically in regenerating species, and
 propose a hypothesis model of interactivity between these pathways that
 may drive regenerative intestinal growth in snakes.
description: Python and Watersnake
 Proteomics DataData tables containing
 peptide spectral matches (PSM) data and additional proteomics data for
 python and watersnake intestine samples at fasted, 1 day post-feeding
 (DPF), and 4 DPF. See included table assigning treatment time points to
 sample/file names.Perry.etal.2019_ProteinDataTables.zip