cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5pt70
title: Data from: Distribution and population structure of the anther smut fungus Microbotryum silenes-acaulis parasitizing an arctic-alpine plant

description: Cold-adapted organisms with current arctic-alpine distributions have
 persisted during the last glaciation in multiple ice-free refugia, leaving
 footprints in their population structure that contrast with temperate
 plants and animals. However, pathogens that live within hosts having
 arctic-alpine distributions have been little studied. Here, we therefore
 investigated the geographical range and population structure of a fungus
 parasitizing an arctic-alpine plant. A total of 1437 herbarium specimens
 of the plant Silene acaulis were examined, and the anther smut pathogen
 Microbotryum silenes-acaulis was present throughout the host’s geographic
 range. There was significantly greater incidence of anther smut disease in
 more northern latitudes and where the host locations were less dense,
 indicating a major influence of environmental factors and/or host
 demographic structure on the pathogen distribution. Genetic analyses with
 seven microsatellite markers on recent collections of 195 M.
 silenes-acaulis individuals revealed three main genetic clusters, in North
 America, northern Europe and southern Europe, likely corresponding to
 differentiation in distinct refugia during the last glaciation. The lower
 genetic diversity in northern Europe indicates postglacial recolonization
 northwards from southern refugia. This study combining herbarium surveys
 and population genetics thus uniquely reveals the effects of climate and
 environmental factors on a plant pathogen species with an arctic-alpine
 distribution.
description: Herbaria-CollectionsResults from herbaria collection of specimens of the plant Silene acaulis partially infected with the pathogen Microbotryum silenes-acaulis. Data has been recorded between 2001 to 2013 from the following herbaria: U.S. Forest Service Herbarium (USFS), New York Botanical Garden (NY), Museum National d'Histoire Naturelle (P), Oregon State University (OSC), University of California, Berkeley (UC), University of Iowa and Iowa State University (ISC), University of Minnesota (MIN), University Washington (WTU), Washington State University (WS), British Museum of Natural History (BM).Microsatellite-DataMicrosatellite data file resulting from genotyping of 255 individuals of Microbotryum silenes-acaulis with 23 markers. Second sheet represents the Structure Input File for the global data set (195 Individuals) analysed with 16 previously developed markers. Third sheet represents the Structure Input File for the Norway/Svalbard Set (110 Individuals) analysed with seven newly-developed markers.
DOI: 10.5061/dryad.d1t81
title: Data from: Context-dependent effects of yolk androgens on nestling growth and immune function in a multibrooded passerine

description: Female birds may adjust their offspring phenotype to the specific
 requirements of the environment by differential allocation of
 physiologically active substances into yolks, such as androgens. Yolk
 androgens have been shown to accelerate embryonic development, growth rate
 and competitive ability of nestlings, but they can also entail
 immunological costs. The balance between costs and benefits of androgen
 allocation is expected to depend on nestling environment. We tested this
 hypothesis in a multibrooded passerine, the spotless starling, Sturnus
 unicolor. We experimentally manipulated yolk androgen levels using a
 between-brood design and evaluated its effects on nestling development,
 survival and immune function. Both in first and replacement broods, the
 embryonic development period was shorter for androgen-treated chicks than
 controls, but there were no differences in second broods. In replacement
 broods, androgen-treated chicks were heavier and larger than those hatched
 from control eggs, but this effect was not observed in the other breeding
 attempts. Androgen exposure reduced survival with respect to controls only
 in second broods. Regarding immune function, we detected nonsignificant
 trends for androgen treatment to activate two important components of
 innate and adaptive immunity (IL-6 and Ig-A levels, respectively).
 Similarly, androgen-treated chicks showed greater lymphocyte proliferation
 than controls in the first brood and an opposite trend in the second
 brood. Our results indicate that yolk androgen effects on nestling
 development and immunity depend on the environmental conditions of each
 breeding attempt. Variation in maternal androgen allocation to eggs could
 be explained as the result of context-dependent optimal strategies to
 maximize offspring fitness.
description: Nestling development
 & ImmunityJEB-2015-00306. Nestling
 development & Immunity.xlsx
DOI: 10.5061/dryad.5h9c4
title: Data from: Projected changes in prevailing winds for transatlantic migratory birds under global warming

description: A number of terrestrial bird species that breed in North America cross the
 Atlantic Ocean during autumn migration when travelling to their
 non-breeding grounds in the Caribbean or South America. When conducting
 oceanic crossings, migratory birds tend to associate with mild or
 supportive winds, whose speed and direction may change under global
 warming. The implications of these changes for transoceanic migratory bird
 populations have not been addressed. We used occurrence information from
 eBird (1950–2015) to estimate the geographical location of population
 centres at a daily temporal resolution across the annual cycle for 10
 transatlantic migratory bird species. We used this information to estimate
 the location and timing of autumn migration within the transatlantic
 flyway. We estimated how prevailing winds are projected to change within
 the transatlantic flyway during this time using daily wind speed anomalies
 (1996–2005 and 2091–2100) from 29 Atmosphere-Ocean General Circulation
 Models implemented under CMIP5. Autumn transatlantic migrants have the
 potential to encounter strong westerly crosswinds early in their
 transatlantic journey at intermediate and especially high migration
 altitudes, strong headwinds at low and intermediate migration altitudes
 within the Caribbean that increase in strength as the season progresses,
 and weak tailwinds at intermediate and high migration altitudes east of
 the Caribbean. The CMIP5 simulations suggest that, during this century,
 the likelihood of autumn transatlantic migrants encountering strong
 westerly crosswinds will diminish. As global warming progresses, the need
 for species to compensate or drift under the influence of strong westerly
 crosswinds during the initial phase of their autumn transatlantic journey
 may be diminished. Existing strategies that promote headwind avoidance and
 tailwind assistance will likely remain valid. Thus, climate change may
 reduce time and energy requirements and the chance of mortality or
 vagrancy during a specific but likely critical portion of these
 species' autumn migration journey.
description: Migration trajectory
 centroidsThe data file contains
 the ten species considered in the study and their daily geographic centers
 of occurrence estimated at the population level daily across the annual
 cycle.centroids.txt
DOI: 10.5061/dryad.t2682
title: Data from: A landscape triage approach: combining spatial and temporal dynamics to prioritize restoration and conservation

description: 1. The spatial and temporal dynamics of landscape structure yield
 ecological constraints that may limit or promote the recovery of
 functioning habitat within human-modified ecosystems. In planning
 restoration and conservation measures to optimize outcomes for
 biodiversity, such constraints should be evaluated at multiple scales. 2.
 This paper presents a multi-scale methodology based on the concept of
 triage that incorporates landscape and regional spatial context and
 temporal dynamics to prioritize restoration and conservation. 3. In
 applying the framework to a large Brazilian Atlantic forest study site
 that underwent substantial forest cover changes between 1990 and 2002, our
 results demonstrate the utility of this framework for navigating between
 different trade-offs inherent to biodiversity conservation. 4. Landscapes
 are ranked in accordance with indicators that evaluate the relative
 urgency of intervention, feasibility of recovery, and importance for
 broader-scale biotic flows. 5. Synthesis and applications. Efforts to
 enhance biodiversity through restoration and/or conservation may be
 hampered when decisions are based exclusively on contemporary landscape
 structure, and not made through a historical perspective. In making such
 trade-offs explicit, this framework can aid practitioners in defining the
 most appropriate set of restoration or conservation strategies given the
 ecological constraints, biodiversity goals, and available budget.
description: Habitat cover,
 connectivity, and forest restoration potential in an Atlantic forest
 regionThis dataset includes a
 set of indices to characterize forest cover and connectivity dynamics,
 which are used to evaluate various aspects of forest restoration potential
 for the 5000-ha focal landscapes distributed across a 1,970,000-ha study
 site in southern Bahia, Brazil for years 1990 and 2002. Refer to the
 corresponding article for a thorough explanation of the indices included
 in this dataset. Both restoration and conservation candidates are
 included.Dataset_Rappaport.zip
DOI: 10.5061/dryad.0d3v5
title: Data from: Genetic structure of the black rhinoceros (Diceros bicornis) in south-eastern Africa

description: Despite an on-going struggle to conserve the endangered black rhinoceros
 (Diceros bicornis) since the 1980’s, huge capital investment and several
 genetic surveys, the level of genetic structure and connectivity among
 populations in southern Africa is not well understood. Here, we undertake
 a major population genetic study of black rhinoceros in the Zimbabwe
 Lowveld, an area inhabited by over half of that country’s original Zambezi
 descendants plus one large population sourced from the relict KwaZulu
 stock of South Africa. Using nuclear microsatellite and mitochondrial DNA
 data, we found much higher levels of genetic diversity in the indigenous
 Zimbabwean populations, where observed multilocus heterozygosity was 0.54
 vs 0.40 in KwaZulu, and maternal haplotype diversity was 0.77 vs 0.03. We
 show, for the first time, that both gene pools can be differentiated from
 each other on the basis of nuclear markers. This, along with the discovery
 of recent gene flow between all Lowveld populations, suggests that
 Zimbabwean and South African gene pools were prehistorically connected.
description: ZimBR_Dyrad_Jul2014
DOI: 10.5061/dryad.r5303
title: Data from: Halfway encounters: meeting points of colonization routes among the southern beeches Nothofagus pumilio and N. antarctica

description: The Patagonian region is characterized by a complex biogeographic history,
 with evidence of deep phylogeographic breaks shared among species. Of
 particular interest to conservation is the nature of colonization and
 settlement patterns after the last glacial period, including the detection
 of secondary contact between different lineages and/or hybridization among
 related species around phylogeographic breaks. Here we studied population
 demography and past hybridization of two widespread tree species endemic
 to South America, Nothofagus pumilio and N. antarctica. Using 8 nuclear
 microsatellites we genotyped 41 populations of both species. Genetic
 variation and structure across the geographic region were evaluated within
 and among species and the past demographic history of hybridization
 between the two species was inferred using Approximate Bayesian
 Computation (ABC). Northern and southern lineages were identified in each
 species, and Bayesian clustering revealed their convergence at mid
 latitudes (42°S). Spatial genetic structure (SGS) also indicated the
 existence of a genetic discontinuity at these latitudes, which is in
 agreement with previous data from maternal DNA markers. Several
 populations around 42–44°S presented high levels of genetic diversity with
 a decrease toward southern populations. Even though the species are
 clearly differentiated (G’ST = 0.335), admixed gene pools were observed in
 both species. Two independent runs of ABC suggested that inter species
 admixture-like patterns occurred within the timescale of the Last Glacial
 Maximum (around 20,000 BP). We also provide evidences of recent and
 bi-directional hybridization/introgression between the two Nothofagus
 species and describe features of the populationś demography in the past.
 The settlement of a secondary contact zone in Nothofagus species around
 42–44°S coincides with the phylogeographic breaks and hotspots of genetic
 diversity found in other plant and animal species in Patagonia,
 highlighting its importance as reservoir of diversity. The
 characterization of the population history of native species can
 contribute substantially to long-term conservation and management
 policies.
description: NpNaInput_MPEThe file contains microsatellites genotypes coming from individuals trees of all populations sampled in the study. Species genotypes are provided in two different sheets.
DOI: 10.5061/dryad.b9h54
title: Data from: Invasion of the Hawaiian Islands by a parasite infecting imperiled stream fishes

description: Points of origin and pathways of spread are often poorly understood for
 introduced parasites that drive disease emergence in imperiled native
 species. Co-introduction of parasites with non-native hosts is of
 particular concern in remote areas like the Hawaiian Islands, where the
 introduced nematode Camallanus cotti has become the most prevalent
 parasite of at-risk native stream fishes. In this study, we evaluated the
 prevailing hypothesis that C. cotti entered the Hawaiian Islands with
 poeciliid fishes from the Americas, and spread by translocation of
 poeciliid hosts across the archipelago for mosquito control. We also
 considered the alternative hypothesis of multiple independent
 co-introductions with host fishes originating from Asia. We inferred
 conduits of introduction and spread of C. cotti across the archipelago
 from geographic patterns of mtDNA sequence variation and allelic variation
 across 11 newly developed microsatellite markers. The distribution of
 haplotypes suggests that C. cotti spread across the archipelago following
 an initial introduction on O'ahu. Approximate Bayesian Computation
 modeling and allelic variation also indicate that O'ahu is the most
 likely location of introduction, from which C. cotti dispersed to Maui
 followed by spread to the other islands in the archipelago. Evidence of
 significant genetic structure across islands indicates that contemporary
 dispersal is limited. Our findings parallel historical records of
 non-native poeciliid introductions and suggest that remediating invasion
 hotspots could reduce the risk of infection in native stream fishes, which
 illustrates how inferences on parasite co-introductions can improve
 conservation efforts by guiding responses to emerging infectious disease
 in species of concern.
description: Camallanus cotti
 genotypesCACO_HI_genotypes.txtCACO-FASTA
DOI: 10.5061/dryad.fg818
title: Data from: Invasion of novel habitats uncouples haplo-diplontic life cycles

description: Baker's Law predicts uniparental reproduction will facilitate
 colonization success in novel habitats. While evidence supports this
 prediction among colonizing plants and animals, few studies have
 investigated shifts in reproductive mode in haplo-diplontic species in
 which both prolonged haploid and diploid stages separate meiosis and
 fertilization in time and space. Due to this separation, asexual
 reproduction can yield the dominance of one of the ploidy stages in
 colonizing populations. We tested for shifts in ploidy and reproductive
 mode across native and introduced populations of the red seaweed
 Gracilaria vermiculophylla. Native populations in the northwest Pacific
 Ocean were nearly always attached by holdfasts to hard substrata and, as
 is characteristic of the genus, haploid–diploid ratios were slightly
 diploid-biased. In contrast, along North American and European coastlines,
 introduced populations nearly always floated atop soft-sediment mudflats
 and were overwhelmingly dominated by diploid thalli without holdfasts.
 Introduced populations exhibited population genetic signals consistent
 with extensive vegetative fragmentation, while native populations did not.
 Thus, the ecological shift from attached to unattached thalli, ostensibly
 necessitated by the invasion of soft-sediment habitats, correlated with
 shifts from sexual to asexual reproduction and slight to strong diploid
 bias. We extend Baker's Law by predicting other colonizing
 haplo-diplontic species will show similar increases in asexuality that
 correlate with the dominance of one ploidy stage. Labile mating systems
 likely facilitate colonization success and subsequent range expansion, but
 for haplo-diplontic species, the long-term eco-evolutionary impacts will
 depend on which ploidy stage is lost and the degree to which asexual
 reproduction is canalized.
description: Gver microsatellite
 genotypesMicrosatellite genotypes
 for all thalliDRYAD_Data.csv
DOI: 10.5061/dryad.4kj53
title: Data from: Host-adapted aphid populations differ in their migratory patterns and capacity to colonize crops

description: Although phytophagous insects can vary genetically in host use and exhibit
 long-range movements, the combined implications of these phenomena for
 pest management have received limited attention. To address this, we
 surveyed the genetic diversity of pea aphid Acyrthosiphon pisum using
 twelve microsatellite loci and assessed host association patterns and
 annual movement from a putative source region (Columbia River Basin) to
 the Palouse region of northern Idaho and western Washington, where the
 aphid is a pest of pea Pisum sativum. A total of 320 identified unique
 genotypes clustered into four genetic groups, with two host plant
 associations: alfalfa Medicago sativa (three genetic groups), and pea
 Pisum sativum and vetch Vicia villosa (one genetic group). All four
 genetic groups occurred in the Columbia River Basin and in migrant aphids
 collected in pan traps during spring colonization in the Palouse during 2
 years of this study. Patterns of group arrival on the Palouse were
 spatially structured early in the season, consistent with differing
 migration patterns. Despite genetic diversity of migrants, a single
 genetic group became predominant in pea crops each year. Clonal laboratory
 colonies of pea aphids established from field-collected specimens and
 representing two predominant genetic groups exhibited reciprocal
 performance trade-offs, with alfalfa being a poor host for a
 pea-associated aphid genotype and vice versa. Synthesis and applications.
 Annual spring migrants of pea aphids in the pea production region of the
 Palouse are genetically diverse, with different host plant affinities
 consistent with origination from source populations in the Columbia River
 Basin. As the season progresses, a single genetic group adapted to pea
 becomes predominant in the crop. Management of pea aphid in the Palouse
 will be improved by monitoring the temporal and spatial variation of
 specific genetic groups of the aphid arriving as immigrants during each
 crop season, providing this information to producers and adjusting
 estimates of risk of crop damage accordingly. The principle could apply to
 other pest species with host-adapted populations that colonize crops on an
 annual basis.
description: Microsatellite
 genotyping - field samplesThe file lists the
 sample location, coordinates, host plant and microsatellite marker
 genotypes for each of the 1100 aphids analyzed for this study. Markers
 used are listed in the paper Materials and Methods.2011 Pantraps and
 SweepsRecord of aphids sampled
 from the Palouse region, from which a subsample was genotyped for the
 study. There is a separate sheet for those sampled in pan traps and those
 sampled by sweep net. Geographic coordinates are provided on one of these
 sheets.2012 Pantraps and
 SweepsAphids collected in pan
 traps and sweep nets during 2012 from which a subsample was genotyped for
 the study. There is a separate sheet for pan and sweep net. One of these
 sheets has the geographic coordinates.
DOI: 10.5281/zenodo.18382165
title: Conformations of experimentally determined carbohydrate 3D structures in the PDB

description: Conformations of High-Quality Curated Carbohydrate Structures in the PDB

(This dataset is published as part of the publication NMETH-RS61001A)

PDB entries are categorized by the type of glycosidic linkages they contain along with a measurement of their φ (Phi), ψ (Psi), and ω (Omega) dihedral angles. The PDB was first filtered for carbohydrates with average B-factors of less than 30 Å2. Further, the PDB data were filtered to remove any highly distorted ring shapes and biologically inconsistent inter-residue linkages.

The definition of the glycosidic dihedral angles is as follows:



for 1-2, 1-3, and 1-4 linkages:φ: C2-C1-OX-CXψ: C1-OX-CX-CX+1




for 1-6 linkages:φ: C2-C1-O6-C6ψ: C1-O6-C6-C5
DOI: 10.5281/zenodo.18382166
title: Conformations of experimentally determined carbohydrate 3D structures in the PDB

description: Conformations of High-Quality Curated Carbohydrate Structures in the PDB

(This dataset is published as part of the publication NMETH-RS61001A)

PDB entries are categorized by the type of glycosidic linkages they contain along with a measurement of their φ (Phi), ψ (Psi), and ω (Omega) dihedral angles. The PDB was first filtered for carbohydrates with average B-factors of less than 30 Å2. Further, the PDB data were filtered to remove any highly distorted ring shapes and biologically inconsistent inter-residue linkages.

The definition of the glycosidic dihedral angles is as follows:



for 1-2, 1-3, and 1-4 linkages:φ: C2-C1-OX-CXψ: C1-OX-CX-CX+1




for 1-6 linkages:φ: C2-C1-O6-C6ψ: C1-O6-C6-C5
DOI: 10.5281/zenodo.18381484
title: White Lightcurves and Spectra for Gordon et al., 2026

description: This tar file contains the transit lightcurves and planet spectra presented in Gordon et al., 2026, "JWST COMPASS: Insights into the Systematic Noise Properties of NIRSpec/G395H From a Uniform Reanalysis of Seven Transmission Spectra (arXix:2511.18196)." The folder 'pca0' corresponds to the '0-vector systematics model' discussed in the paper, and the folder 'pca6' corresponds to the '6-vector systematics model' from the paper. 

 

The white-light light curve and spectrum file names are all prefixed by the TESS Object of Interest identifier, i.e.




TOI
Object


134.01
L 168-9 b


175.01
L 98-59 c


562.01
GJ 357 b


776.01
TOI-776 c


776.02
TOI-776 b


836.01
TOI-836 c


836.02
TOI-836 b
DOI: 10.5281/zenodo.18381483
title: White Lightcurves and Spectra for Gordon et al., 2026

description: This tar file contains the transit lightcurves and planet spectra presented in Gordon et al., 2026, "JWST COMPASS: Insights into the Systematic Noise Properties of NIRSpec/G395H From a Uniform Reanalysis of Seven Transmission Spectra (arXix:2511.18196)." The folder 'pca0' corresponds to the '0-vector systematics model' discussed in the paper, and the folder 'pca6' corresponds to the '6-vector systematics model' from the paper. 

 

The white-light light curve and spectrum file names are all prefixed by the TESS Object of Interest identifier, i.e.




TOI
Object


134.01
L 168-9 b


175.01
L 98-59 c


562.01
GJ 357 b


776.01
TOI-776 c


776.02
TOI-776 b


836.01
TOI-836 c


836.02
TOI-836 b