cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nzs7h44t7
title: Supplementary alignment, phylogenetic, and biogeographic analysis data for: Phylogenomics of Gars

description: Reconstructing deep-time biogeographic histories is limited by the
 comparatively recent diversification of most extant lineages. Ray-finned
 fishes (Actinopterygii), which include more than half of living
 vertebrates, are no exception. Although many of the most species-rich
 clades of ray-finned fishes diversified after the Cretaceous-Paleogene
 mass extinction, a handful of ancient and species-depauperate lineages
 persist today. One of the most iconic ancient lineages of ray-finned
 fishes are gars, a clade of seven freshwater species restricted to
 continental North America and Cuba. Here, we use DNA sequences of more
 than 1,000 exons collected for all living species of gars and a
 morphological dataset that includes 16 fossil species to infer their
 phylogenetic relationships and estimate divergence times using fossil-tip
 dated relaxed molecular clock analyses. Our analyses show that the two
 major lineages of living gars, Atractosteus and Lepisosteus, diverged
 approximately 105 million years ago. Using the time-calibrated phylogeny
 of the living and fossil gar species and model-based biogeographic
 reconstructions, we find that many of the inferred vicariant events in the
 evolutionary history of gars closely track the Mesozoic fragmentation of
 Laurasia in the Northern Hemisphere and the Cretaceous reorganization of
 North American river drainage systems. In particular, we tie the initial
 diversification of living gars to the expansion of the early Atlantic and
 subsequent loss of shallow marine habitat between the Americas and Africa
 in the Cretaceous. All living gar species originated after the Cretaceous
 in eastern North America, implying that this region has both served as the
 ancestral area of extant gar diversity and a refugium of this iconic
 ancient vertebrate lineage.
DOI: 10.5061/dryad.0vt4b8h1h
title: Data for: Telomere length is highly repeatable and shorter in individuals with more elaborate sexual ornamentation in a short-lived passerine

description: Quantifying an individual’s state as fitness proxy has proven challenging,
 but accumulating evidence suggests that telomere length and attrition may
 indicate individual somatic state and success at self-maintenance,
 respectively. Sexual ornamentation is also thought to signal phenotypic
 quality, but links between telomeres and sexual ornamentation have been
 little explored. To address this issue, we examined whether telomere
 length and dynamics are predicted by the expression of a sexually selected
 ornament, the length of the outermost tail feathers (streamers), using
 longitudinal data from a population of European barn swallows (Hirundo
 rustica). In 139 adult individuals, each measured twice, we further
 assessed associations of telomere length with age, sex, breeding status
 and survival. Telomere length showed high individual repeatability (R =
 0.97) across years while shortening with age in both sexes. Telomere
 length and dynamics were not significantly associated with survival to the
 next year, remaining lifespan, or reproduction status (comparing breeding
 and non-breeding yearlings). Tail streamer length, a sexually selected
 trait in barn swallows, was negatively associated with telomere length,
 independent of sex. Thus, telomere length may reflect the costs of
 carrying an elaborated sexual ornament, although ornament size did not
 significantly predict telomere shortening. In conclusion, telomere length
 in adult barn swallows is a highly consistent trait that shows a negative
 relationship with sexual ornamentation, suggesting a trade-off between
 sexual ornamentation and telomere length.
DOI: 10.5281/zenodo.16787720
title: table S1

description: supplementary file
DOI: 10.5281/zenodo.16787719
title: table S1

description: supplementary file
DOI: 10.5281/zenodo.18309725
title: Catalina 500 LIBS data

description: LIBS data acquired during the EXCITE measurement campaign in November 2025 on a meteorite sample Catalina 500. The acquisition details are collected in the metadata.txt file.
DOI: 10.5281/zenodo.18309726
title: Catalina 500 LIBS data

description: LIBS data acquired during the EXCITE measurement campaign in November 2025 on a meteorite sample Catalina 500. The acquisition details are collected in the metadata.txt file.
DOI: 10.5061/dryad.m905qfv2z
title: Data from: Deep genome‐wide phylogeographic structure indicates cryptic diversity in the Middle Spotted Woodpecker (Dendrocoptes medius)

description: Deep phylogeographic structure in mitochondrial DNA not reflected in
 morphological variation has been uncovered in a number of species over the
 past few decades. However, inferred phylogeographic structure based solely
 on mitochondrial DNA can be misleading and might not reflect the true
 history of evolutionary lineages. Consequently, such cases should be
 further investigated based on genome‐wide data. One of these examples is
 provided by the Middle Spotted Woodpecker Dendrocoptes medius, a
 non‐migratory habitat specialist associated with old deciduous forests of
 the Western Palaearctic. It displays strong genetic divergence in
 mitochondrial DNA between Asian and European populations despite there
 being only slight variation in morphology between them. Here, we found a
 clear genomic divergence between Asian and European populations that is
 consistent with mitochondrial divergence patterns. As revealed by
 isolation by distance analyses, this differentiation in two lineages was
 not merely an effect of geography. Genomic population structure indicates
 that both the Asian and European lineages might each have been separated
 in more than one refugium during the last glacial maximum. The Middle
 Spotted Woodpecker might represent a case of cryptic diversity throughout
 its distribution range, as has been previously found for other taxa across
 the tree of life. However, we also found footprints of gene flow from the
 Asian into the European populations, suggesting at least limited
 introgression upon secondary contact. The processes and mechanisms that
 might prevent lineage fusion between the morphologically cryptic but
 genetically divergent lineages of the Middle Spotted Woodpecker need to be
 further investigated especially in the area of potential secondary
 contact.
description: # Deep genome-wide phylogeographic structure indicates cryptic diversity
 in the middle spotted woodpecker Dendrocoptes medius
 [https://doi.org/10.5061/dryad.m905qfv2z](https://doi.org/10.5061/dryad.m905qfv2z) ## Description of the data and file structure Beagle format file of filtered SNPs The file Woodpecker57_Maf0.01_GL2.beagle.gz contains the filtered SNPs from the GBS dataset of 57 middle spotted woodpecker individuals. SNPs were called and genotyped using angsd with filetering parameters: a maximum p-value of 10−3 for being variable, a minimum mapping quality of 20, a minimum base quality score of 20, a minimum total read depth of 120, a minimum individual read depth of 5 and a minimum minor allele frequency of 0.01 (-SNP_pval 1e-3 -minQ 20 -minMapQ 20 -setMinDepth 120 -geno_minDepth 5 -minMaf 0.01).
DOI: 10.5061/dryad.fbg79cnwk
title: Genome-wide sequence data show no evidence of hybridization and introgression among pollinator wasps associated with a community of Panamanian strangler figs

description: The specificity of pollinator host choice influences opportunities for
 reproductive isolation in their host plants. Similarly, host plants can
 influence opportunities for reproductive isolation in their pollinators.
 For example, in the fig and fig wasp mutualism, offspring of fig
 pollinator wasps mate inside the inflorescence that the mothers pollinate.
 Although often host specific, multiple fig pollinator species are
 sometimes associated with the same fig species, potentially enabling
 hybridization between wasp species. Here we study the 19 pollinator
 species (Pegoscapus spp.) associated with an entire community of
 16 Panamanian strangler fig species (Ficus subgenus Urostigma,
 section Americanae) to determine whether the previously documented history
 of pollinator host switching and current host sharing predicts genetic
 admixture among the pollinator species, as has been observed in their host
 figs. Specifically, we use genome-wide ultraconserved element (UCE) loci
 to estimate phylogenetic relationships and test for hybridization and
 introgression among the pollinator species. In all cases, we recover
 well-delimited pollinator species that contain high interspecific
 divergence. Even among pairs of pollinator species that currently
 reproduce within syconia of shared host fig species, we found no evidence
 of hybridization or introgression. This is in contrast to their host figs,
 where hybridization and introgression have been detected within this
 community, and more generally, within figs worldwide. Consistent with
 general patterns recovered among other obligate pollination mutualisms
 (e.g., yucca moths and yuccas), our results suggest that while
 hybridization and introgression are processes operating within the host
 plants, these processes are relatively unimportant within their associated
 insect pollinators.
DOI: 10.5061/dryad.cfxpnvx6x
title: Phylogeography and genetic variation in Western Jacob's ladder (Polemonium occidentale) provide insights into the origin and conservation of rare species in the Great Lakes region

description: The perennial herb Western Jacob’s Ladder (Polemonium occidentale,
 Polemoniaceae) is widespread in the mountains of western North America but
 reappears as a disjunct in the Great Lakes Region in Minnesota and
 Wisconsin, USA as the narrow endemic P. occidentale subsp. lacustre. This
 distribution is shown by a diverse assemblage of angiosperms. It has been
 hypothesized that these species became isolated just after the Last
 Glacial Maximum, but this has not been tested. Additionally, the genetic
 diversity and population connectivity of the endemic Great Lakes flora has
 been understudied, with important conservation implications. Using
 Genotyping-by-sequencing, we examined the relationship of P. occidentale
 subsp. lacustre to its closest relatives, relationships among all known
 populations, and genetic diversity within these populations. Polemonium
 occidentale subsp. lacustre represents an isolated, unique lineage that
 diverged from its closest relatives 1.3 ma and arrived in the Great Lakes
 Region by at least 38 ka. Nearly all extant populations diverged prior to
 the Last Glacial Maximum, are largely genetically distinct, and show
 relatively little within-population genetic diversity. Clonality may
 mitigate reduction in diversity due to drift. Mixed population signal
 between Wisconsin and some Minnesota populations may be due to gene flow
 during the Late Pleistocene. While populations of Polemonium occidentale
 subsp. lacustre may be relictual from a now-extinct western relative, it
 is best treated as a distinct species. Conservation efforts should focus
 more on ensuring that current populations remain rather than maintaining
 large population sizes across a few populations. However, encouraging
 habitat heterogeneity may accomplish both simultaneously.
DOI: 10.5061/dryad.n5tb2rbxd
title: Synthesis of batrachochytrium dendrobatidis infection in South America: amphibian species under risk and areas to focus research and disease mitigation

description: Amphibian chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd),
 has been recognized as the infectious disease causing the most
 catastrophic loss of biodiversity known to science, with South America
 being the most impacted region. We tested whether Bd prevalence is
 distributed among host taxonomy, ecoregion, conservation status and
 habitat preference in South America. Here we provide a synthesis on the
 extent of Bd infection across South America based on 21,648 molecular
 diagnostic assays, roles of certain species in the epidemiology of Bd and
 explore its association with the reported amphibian catastrophic declines
 in the region. We show that Bd is widespread, with a continental
 prevalence of 23.2%. Its occurrence in the region shows a phylogenetic
 signal and the probability of infection is determined by ecoregion,
 preferred habitat, and extinction risk hosts’ traits. The taxa exhibiting
 highest Bd occurrence, were mostly aquatic amphibians, including Ranidae,
 Telmatobiidae, Hylodidae, Calyptocephalellidae and Pipidae. Surprisingly,
 families exhibiting unusually low Bd prevalence included species in which
 lethal chytridiomycosis and population declines have been described (genus
 Atelopus, Rhinoderma and Eleutherodactylus). Higher than expected
 prevalence of Bd occurred mainly in amphibians living associated with
 mountain environments in the Andes and Atlantic forests, reflecting highly
 favourable Bd habitats in these areas. Invasive amphibian species (e.g.
 Lithobates catesbeianus and Xenopus laevis) exhibited high Bd prevalence,
 as thus we suggest using these as sentinels to understand their potential
 role as reservoirs, vectors or spreaders of Bd that can be subjected to
 management. Our results guide on the prioritization of conservation
 actions to prevent further biodiversity loss due to chytridiomycosis in
 the world’s most amphibian diverse region.
description: Literature review and own non-published data.
DOI: 10.5061/dryad.9kd51c5jz
title: Microbial diversity patterns at three swimming beaches in La Jolla, CA

description: This dataset contains Illumina MiSeq sequencing reads produced during a
 community-initiated study of marine microbial diversity in La Jolla,
 California. The three collection sites, all popular swimming beaches, are
 notable for their differences in human activity and marine wildlife. 16S
 V4 rDNA sequencing of planktonic bacteria followed by diversity analysis
 in Qiime2 showed that La Jolla Cove and the La Jolla Children's Pool
 have significantly higher OTU diversity than La Jolla Shores. All three
 sites have distinct taxonomic composition. No evidence of pathogenic
 bacteria was found. This study is an example of low-budget,
 community-driven science that uses state-of-the-art DNA sequencing methods
 to advance our understanding of coastal environments.
description: <strong>180312_Hyland_S0_L001_I1_001.fastq.gz</strong> gzip-compressed FASTQ file containing barcode sequences for each read <strong>180312_Hyland_S0_L001_R1_001.fastq.gz</strong> gzip-compressed FASTQ file containing FORWARD read sequences and quality scores <strong>180312_Hyland_S0_L001_R2_001.fastq.gz</strong> gzip-compressed FASTQ file containing REVERSE read sequences and quality scores <strong>180312_Hyland_metadata.txt</strong> Tab-separated file containing sequencing information and standard metadata fields for the Earth Microbiome Project (EMP). See <strong>README_180312_Hyland.txt</strong> for descriptions of metadata fields
DOI: 10.6076/d14g68
title: DEPP: Deep learning enables extending species trees using single genes

description: Placing new sequences onto reference phylogenies is increasingly used for
 analyzing environmental samples, especially microbiomes. However, existing
 placement methods have a fundamental limitation: they assume that query
 sequences have evolved using specific models directly on the reference
 phylogeny. Thus, they can place single-gene data (e.g., 16S rRNA
 amplicons) onto their own gene tree. This practice is a proxy for a more
 ambitious goal: extending a (genome-wide) species tree given data from
 individual genes. No algorithm currently addresses this challenging
 problem. Here, we introduce Deep-learning Enabled Phylogenetic Placement
 (DEPP), an algorithm that learns to extend species trees using single
 genes without pre-specified models. We show that DEPP updates the
 multi-locus microbial tree-of-life with single genes with high accuracy.
 We further demonstrate that DEPP can achieve the long-standing goal of
 combining 16S and metagenomic data onto a single tree, enabling community
 structure analyses that were previously impossible and producing robust
 patterns.
description: Please note, this dataset is the most recent version of a
 duplicate dataset available via this link: https://doi.org/10.6076/D1JS3Z (published February 4, 2022).
DOI: 10.5061/dryad.0gb5mkm2x
title: Improving dryland seedling recruitment using fungicide seed coatings

description: The success of seed-based restoration in dryland regions of the world is
 often low or sporadic, with most mortality occurring between germination
 and emergence. Fungal pathogenesis is one process that may reduce seedling
 emergence and limit restoration success. Our objective was to determine
 whether fungicide seed coatings constitute an economically viable strategy
 for increasing emergence by reducing fungal pathogenesis and mortality. We
 performed an experiment across two sites and three years, using bluebunch
 wheatgrass (Pseudoroegneria spicata) as a model species. We found that
 fungicide coatings increased germination by 8.8% and emergence by 54.0% on
 average compared to the control. A cost analysis indicated that the
 fungicide coating was economically viable with an average estimated
 effective cost reduction of 18.8% under the study conditions. There was a
 strong interaction (P &lt; 0.001) between the effects of the fungicide
 coating, site, and year on emergence. The fungicide coating increased
 emergence compared to the control in five of the six sites and years, with
 the effect ranging from a 33.7% decrease (P = 0.042) to a 150.9% increase
 (P = 0.004). The observed interaction was likely related to the effect of
 the hydrothermal microsite environment on disease severity. In the site
 and year that the fungicide coating performed worse than the control,
 prolonged periods of exceptionally low soil moisture may have reduced
 disease severity through a variety of individual and community scale
 mechanisms. Overall, these results indicate that fungicide seed coatings
 have the potential to improve dryland restoration efforts.
DOI: 10.5061/dryad.59zw3r294
title: Data supplement to: Plant proxy evidence for high rainfall and productivity in the eocene of Australia

description: During the early to middle Eocene, a mid-to-high latitudinal position and
 enhanced hydrological cycle in Australia would have contributed to a
 wetter and “greener” Australian continent where today arid to semi-arid
 climates dominate. Here, we revisit 12 Australian plant megafossil sites
 from the early to middle Eocene to generate temperature, precipitation and
 seasonality paleoclimate estimates, as well as net primary productivity
 (NPP) and vegetation type, based on paleobotanical proxies and compare to
 early Eocene global climate models. Temperature reconstructions are
 uniformly subtropical (mean annual, summer, and winter mean temperatures
 19–21 °C, 25–27 °C and 14–16 °C, respectively). This indicates that
 southern Australia was ~5 °C warmer than today, despite a &gt;20°
 poleward shift from its modern geographic location. Precipitation was less
 homogeneous than temperature, with mean annual precipitation of ~60 cm
 over inland sites and &gt;100 cm over coastal sites. Precipitation may
 have been seasonal with the driest month receiving between 2–7× less
 precipitation as mean monthly precipitation. Proxy-model comparison is
 favorable with an 1680 ppm CO2 concentration. However, individual proxy
 reconstructions can disagree with models as well as with each other. In
 particular, seasonality reconstructions have systemic offsets. NPP
 estimates were up to 1000 gC m-2 yr-1 higher than modern, implying a more
 homogenously “green” Australian continent in the early to middle Eocene
 and larger carbon fluxes to and from the Australian biosphere. The most
 similar modern vegetation type is modern-day eastern Australian
 subtropical forest, although distance from coast and latitude may have led
 to vegetation heterogeneity.
description: Includes: <strong>TABLE S1: Physiognomic
 information of modern floral calibration sites and Australian Eocene
 fossil sites</strong> <strong>TABLE S2:
 Modern calibration CCA scores; vector scores and climate; used to
 calculate regression equations to calculate paleoclimate of fossil
 sites.</strong> <strong>TABLE S3: Modern
 calibration sites in northern Australia for LAA Eqn
 4</strong> <strong>TABLE S4: Average of
 natural log of leaf sizes at each locality used in Leaf Area
 Analysis</strong> <strong>TABLE S5: Leaf
 margin percentage and number of leaf types per site; used in Leaf Margin
 Analysis</strong> <strong>TABLE S6: Taxa
 recorded at fossil site; their modern climatic niche and raw distribution
 data link (GBIF DOI)</strong> <strong>TABLE
 S7: Raw climatic output from point extractions of DeepMIP Global
 Circulation Models at different CO2 levels</strong>
DOI: 10.5061/dryad.ffbg79cwn
title: A dataset for pollinator diversity and their interactions with plants in the Pacific NorthWest

description: Pollinator populations have declined substantially in recent years. The
 resulting loss in pollination services has both ecological and economic
 consequences including reductions in plant diversity and crop production
 and lower food security. Datasets that identify pollinators and their
 plant hosts are of utmost importance in order to understand the main
 causes of pollinator declines. Here we present a dataset, which contains
 67,954 individual pollinator records. The data has been collected across
 the Pacific Northwest, primarily focused in British Columbia (Canada),
 with 182 individual sites over 11 years, between 2005 and 2017. This
 dataset comprises multiple studies that aimed to collect information on
 pollinator abundance, diversity and their interactions with plants.
 Overall, the dataset includes 937 morphospecies (of which 482 were
 identified to species) of pollinators across 105 families, including data
 for bees, wasps, butterflies, moths and flies. We also present information
 on the interactions of these species, with 473 species of plants. This
 data set is released for non-commercial use only. Credits should be given
 to this paper (i.e., proper citation). 
description: <strong>Pan
 trapping </strong> 350ml pan
 traps were set out along 100 meter parallel transects at 10 metre
 intervals for 7.5-8.5 hours per day. Each study used an equivalent number
 of blue, white, and yellow pan traps per transect.  Netting Three types of netting surveys were used in these
 studies, single-plant-surveys, all-plant-surveys and transect
 methods. “Single-Plant-Survey” by
 Plot: Conducted 10min netting surveys on each plant species in bloom
 within 1ha area. Stopping timer to process captured insects. Collectors
 conducted two 10min surveys per plant species within a surveying round.
 Sites were sampled multiple times throughout the season depending on the
 study. “All-Plant-Survey” by plot:
 Two collectors conducted 15 or 20 or 30 min netting surveys on all plants
 within a 1ha area. Sites were sampled multiple times throughout the season
 depending on the study. “Transect
 method”: Collectors conducted 10min netting surveys on 3 or 4 transects
 that were 50 or 100m in length. Collectors visited sites 2 to 5 times
 during the flowering season. Two studies only observed blueberry bushes
 and one study included other plant species. Each study conducted unique
 randomization techniques for netting within fields. For both pan trapping and netting methods all
 pollinators were collected for identification in the lab.
DOI: 10.15468/dl.6z743r
title: Occurrence Download

description: A dataset containing 704 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pseudocoladenia dan"
 ]
}

 The dataset includes 704 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003036-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.