cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d7wm37pz9
title: Monthly pCO2, gas transfer velocity and CO2 efflux rate in global streams and rivers (the GRADES river networks)

description: The datasets contain monthly partial pressure of
 dissolved CO2 (pCO2, µatm), gas transfer velocity (k, m d-1), and
 CO2 efflux rate (g C m-2 d-1) estimates for global streams and rivers in
 both comma separated values (csv) and GeoTIFF formats. These datasets
 served as the base for monthly CO2 emission estimates for global streams
 and rivers and can be used to support regional terrestrial carbon
 balances. Original vector-version of products is based
 on the Global Reach–level A priori Discharge Estimates for SWOT
 or GRADES river networks, which have ~ 3 million individual
 reaches of global streams and rivers. The GeoTIFF
 version has a spatial resolution of approximately
 0.0083º (1 km). The datasets also contain direct CO2 measurements
 compiled from the literature (Supplementary Data 1).
description: TheGlobal Reach–level A priori Discharge Estimates for SWOT
 or GRADES river networks and associated river-reach slope and length
 estimates can be found
 at http://hydrology.princeton.edu/data/mpan/MERIT_Basins/. The GRADES
 daily discharge estimates can be found
 at http://hydrology.princeton.edu/data/mpan/GRADES/. Monthly river widths
 can be estimated utilizing the GRADES annual and monthly mean discharge,
 and downstream and at-a-station hydraulic geometry developed for each of
 the wetness conditions. Length, width and surface area are aggregaged to
 78 cross-region basins based on hydrology and flow regime for stream
 order extrapolation (to an end width of 0.3 m). Total surface area of a
 basin is the sum of the surface area represented by the GRADES river
 networks and the extrapolated area. Both the GRADES and the
 extrapolated surface areas are corrected for loss due to temporal drying
 up and ice coverages. CO<sub>2</sub> flux
 is the product of dissolved CO<sub>2</sub> concentration
 (converted from <em>p</em>CO<sub>2</sub> according
 to Henry's Law), gas transfer velocity (<em>k</em>) and
 stream/river surface area. CO<sub>2</sub> flux can be
 calculated for each river reach of the GRADES river networks and each
 stream order for the extrapolated area. Total CO<sub>2</sub>
 emission from streams and rivers in a basin is the sum of
 CO<sub>2</sub> emission from the GRADES river reaches and
 extrapolated river surface area, taking into account both losses from both
 ephemeral streams and ice covered periods. Relevant codes are available at
 https:///github.com/lsdeel/globalRiverCO2emission.
DOI: 10.5061/dryad.7wm37pvq9
title: Gibbon genome (Nleu3.0) custom gene annotation file

description: Co-option of transposable elements (TEs) to become part of existing or new
 enhancers is an important mechanism for evolution of gene regulation.
 However, contributions of lineage-specific TE insertions to recent
 regulatory adaptations remain poorly understood. Gibbons present a
 suitable model to study these contributions as they have evolved a
 lineage-specific TE called LAVA, which is still active in the gibbon
 genome. The LAVA retrotransposon is thought to have played a role in the
 emergence of the highly rearranged structure of the gibbon genome by
 disrupting transcription of cell cycle genes. In this study, we
 investigated whether LAVA may have also contributed to the evolution of
 gene regulation by adopting enhancer function. We characterized fixed and
 polymorphic LAVA insertions across multiple gibbons and found 96 LAVA
 elements overlapping enhancer chromatin states. Moreover, LAVA was
 enriched in multiple transcription factor binding motifs, was bound by an
 important transcription factor (PU.1), and was associated with higher
 levels of gene expression in cis. We found gibbon-specific signatures of
 purifying/positive selection at 27 LAVA insertions. Two of these
 insertions were fixed in the gibbon lineage and overlapped with enhancer
 chromatin states, representing putative co-opted LAVA enhancers. These
 putative enhancers were located within genes encoding SETD2 and RAD9A, two
 proteins that facilitate accurate repair of DNA double-strand breaks and
 prevent chromosomal rearrangement mutations. Co-option of LAVA in these
 genes may have influenced regulation of processes that preserve genome
 integrity. Our findings highlight the importance of considering
 lineage-specific TEs in studying evolution of novel gene regulatory
 elements.
DOI: 10.6078/d10d8f
title: The theory and applications of measuring broad-range and chromosome-wide recombination rate from allele frequency decay around a selected locus

description: Abstract Recombination is the exchange of genetic material between
 homologous chromosomes via physical crossovers. High throughput sequencing
 approaches detect crossovers genome-wide to produce recombination rate
 maps but are difficult to scale as they require large numbers of
 recombinants individually sequenced. We present a simple and scalable
 pooled-sequencing approach to experimentally infer near chromosome-wide
 recombination rates by taking advantage of non-Mendelian allele frequency
 generated from a fitness differential at a locus under selection. As more
 crossovers decouple the selected locus from distal loci, the distorted
 allele frequency attenuates distally towards Mendelian and can be used to
 estimate the genetic distance. Here, we use marker selection to generate
 distorted allele frequency and theoretically derive the mathematical
 relationships between allele frequency attenuation, genetic distance, and
 recombination rate in marker selected pools. We implemented nonlinear
 curve fitting methods that robustly estimate the allele frequency decay
 from batch sequencing of pooled individuals, and derive chromosome-wide
 genetic distance and recombination rates. Empirically, we show that marker
 selected pools closely recapitulate genetic distances inferred from
 scoring recombinants. Using this method, we generated novel recombination
 rate maps of three wild derived strains of Drosophila melanogaster, which
 strongly correlate with previous measurements. Moreover, we show that this
 approach can be extended to estimate chromosome-wide crossover
 interference with reciprocal marker selection and discuss how it can be
 applied in the absence of visible markers. Altogether, we find that our
 method is a simple and cost-effective approach to generate chromosome-wide
 recombination rate maps requiring only one or two libraries.
DOI: 10.5061/dryad.80gb5mkp0
title: Data from: Molecular square dancing in CO-CO collisions

description: Knowledge of rotational energy transfer (RET) involving carbon monoxide
 (CO) molecules is crucial for the interpretation of astrophysical data. As
 of now, our nearly perfect understanding of atom-molecule scattering shows
 that RET usually occurs by only a simple “bump” between partners. To
 advance molecular dynamics to the next step in complexity, we studied
 molecule-molecule scattering in great detail for collision between two CO
 molecules. Using advanced imaging methods and quasi-classical and fully
 quantum theory, we found that a synchronous movement can occur during
 CO-CO collisions, whereby a bump is followed by a move similar to a
 “do-si-do” in square dancing. This resulted in little angular deflection
 but high RET to both partners, a very unusual combination. The associated
 conditions suggest that this process can occur in other molecule-molecule
 systems.
description: Collision between two carbon monoxide (CO) molecules at a
 collision energy of 1460 cm<sup>-1</sup> has been investigated
 by measuring velocity-map ion images for rotationally excited CO molecules
 using a crossed molecular beam apparatus in combination with a VUV (Vacuum
 Ultra-Violet) REMPI (Resonance Enhanced Multi Photon Ionization) scheme.
 Partially resolved pair-correlated differential cross sections
 (PC-DCSs) were extracted for analysis of the radius-dependent
 angular distribution of the image using an onion-peeling inversion
 procedure.  The experimental results of this analysis
 were compared with advanced theory, in particular with the
 predictions of QCT (Quasi-Classical Trajectory) calculations, and
 good agreement between experiment and theory was found. An extraordinary
 energy transfer channel is revealed, featuring forward scattering while
 both CO product molecules are highly rotationally excited, which defies
 prediction from prevailing models of inelastic scattering. An
 extraordinary energy transfer channel is revealed, featuring forward
 scattering while both CO product molecules are highly rotationally
 excited, which defies prediction from prevailing models of inelastic
 scattering.  Simulation by quasi-classical trajectories on an accurate
 intermolecular potential energy surface and opacity function analysis show
 that these unusual product events start with the large C ends of CO
 colliding with each other, with immediate and large transfer from
 translational to rotational energy.  This
 forward-scattered-symmetric-excitation behaviour was also cinfirmed
 by Quantum Close-Coupling calculations.
DOI: 10.5061/dryad.s1rn8pk50
title: Large-scale phylogenomics reveals ancient introgression in Asian Hepatica and new insights into the origin of the insular endemic Hepatica maxima

description: Hepatica maxima is native to Ulleungdo, which is one of the
 oceanic islands in Korea, and it likely originated via anagenetic
 speciation from the Korean mainland species H. asiatica. However,
 the relationships among the Asian lineages remain unresolved.
 Phylogenomics based on plant genomes can provide new insights into the
 evolutionary history of plants. We first generated plastid, mitochondrial
 and transcriptome sequences of the insular endemic species H.
 maxima. Using the genomic data for H. maxima, we obtained a
 phylogenomic dataset consisting of 76 plastid, 37 mitochondrial and 413
 nuclear genes from Asian Hepatica and two outgroups.
 Coalescent- and concatenation-based methods revealed cytonuclear and
 organellar discordance in the lineage. The presence of gynodioecy with
 cytoplasmic male sterility in Asian Hepatica suggests
 that the discordance is correlated with potential disruption of linkage
 disequilibrium between the organellar genomes. Species network analyses
 revealed a deep history of hybridization and introgression in
 Asian Hepatica. We discovered that ancient and recent
 introgression events occurred throughout the evolutionary history of the
 insular endemic species H. maxima. The introgression may serve as
 an important source of genetic variation to facilitate adaptation to the
 Ulleungdo environment.
DOI: 10.5061/dryad.w6m905qmm
title: Data from: A synthesis of the coast-wide decline in survival of west coast Chinook salmon (Oncorhynchus tshawytscha, Salmonidae)

description: We collated smolt-to-adult return rate (SAR) data for Chinook salmon from
 all available regions of the Pacific coast of North America to examine the
 large-scale patterns of salmon survival.  For consistency, our
 analyses primarily used coded wire tag-based (CWT) SAR estimates.
  Survival collapsed over the past half century by roughly a
 factor of three to ca. 1% for many regions.  Within the Columbia
 River, the SARs of Snake River populations, often singled out as exemplars
 of poor survival, are unexceptional and in fact higher than estimates
 reported from many other regions of the west coast lacking dams.
  Given the seemingly congruent decline in SARs to similar levels,
 the notion that contemporary survival is driven primarily by broader
 oceanic factors rather than local factors should be considered.
  Ambitious Columbia River rebuilding targets may be unachievable
 because other regions with nearly pristine freshwater conditions, such as
 SE Alaska and northern BC, also largely fail to reach these levels.
  Passive integrated transponder (PIT) tag-based SAR estimates
 available for Columbia River basin populations are generally consistent
 with CWT findings; however, PIT tag-based SARs are not adjusted for
 harvest which compromises their intended use because harvest rates are
 large and variable. More attention is needed on how SARs should be
 quantified and how rebuilding targets are defined.  We call for a
 systematic review by funding agencies to assess consistency and
 comparability of the SAR data generated and to further assess the
 implications of survival falling to similar levels in most regions of the
 west coast.
description: Contains the compilation of the survival-to-adult return (SAR)
 data for Chinook salmon used in the publication. See Table S1 from the
 publication for definition of fields and citations.  The data was compiled
 from several intergovernmental organizations which did the original
 collation and data aggregation.  The data we provide here are to document
 our own analyses for those interested in verifying the findings.  However,
 the original databases should be taken as the source for the most
 up-to-date data, as the data for the most recent years is occassionally
 updated.
description: There are no missing values.  See the header row in each data
 file for source information.
DOI: 10.5061/dryad.g79cnp5mt
title: The palaeoendemic conifer Pherosphaera hookeriana (Podocarpaceae) exhibits high genetic diversity despite Quaternary range contraction and post glacial bottlenecking

description: Glacial relict plants are often endangered because extant populations can
 be small, geographically isolated and persist in suboptimal environments,
 leading to increased clonality and reduced genetic diversity putting their
 survival at further risk.  This study examines how restriction to
 interglacial refugia has impacted the genetic diversity and structure of
 the threatened Tasmanian palaeoendemic, Pherosphaera hookeriana W. Archer
 bis.  This species is a poorly dispersed, dioecious conifer that,
 having once been a major component of Last Glacial vegetation, is now
 limited to 30 known populations.  Genetic diversity and structure
 were assessed using fifteen nuclear and nine chloroplast SSRs in 23
 populations representing the species’ entire range.  Changes in
 distribution and abundance from the Last Glacial to present were
 investigated by examining the fossil record, approximate Bayesian
 computation (ABC) and species distribution modelling.  Despite
 fossil and ABC based evidence for a postglacial bottleneck, species-level
 genetic diversity (He = 0.56 and Ne = 2.86) exceeded that of some conifers
 with far wider distributions.  Significant genetic structure (Fst
 = 0.127, Jost’s D = 0.203) was present, with most populations dominated by
 distinct nuclear SSR genetic clusters and having unique chloroplast
 haplotypes.  Unexpectedly, clonality plays only a small role in
 population level regeneration.  Genetic diversity has likely been
 maintained due to dioecy, persistence in multiple parts of its range and
 extant populations being directly descended from proximate glacial
 populations.  Protecting populations from the mounting threat of
 fire will remain crucial for the in situ conservation of P.
 hookeriana.
DOI: 10.5061/dryad.qbzkh18f7
title: Chromosomal-level genome assembly of the scimitar‐horned oryx: insights into diversity and demography of a species extinct in the wild

description: Captive populations provide a valuable insurance against extinctions in
 the wild. However, they are also vulnerable to the negative impacts of
 inbreeding, selection and drift. Genetic information is therefore
 considered a critical aspect of conservation management. Recent
 developments in sequencing technologies have the potential to improve the
 outcomes of management programmes; however, the transfer of these
 approaches to applied conservation has been slow. The scimitar‐horned oryx
 (Oryx dammah) is a North African antelope that has been extinct
 in the wild since the early 1980s and is the focus of a large‐scale and
 long‐term reintroduction project. To enable the selection of suitable
 founder individuals, facilitate post‐release monitoring and improve
 captive breeding management, comprehensive genomic resources are required.
 Here, we used 10X Chromium sequencing together with Hi‐C contact mapping
 to develop a chromosomal‐level genome assembly for the species. The
 resulting assembly contained 29 chromosomes with a scaffold N50 of 100.4
 Mb, and displayed strong chromosomal synteny with the cattle genome. Using
 resequencing data from six additional individuals, we demonstrated
 relatively high genetic diversity in the scimitar‐horned oryx compared to
 other mammals, despite it having experienced a strong founding event in
 captivity. Additionally, the level of diversity across populations varied
 according to management strategy. Finally, we uncovered a dynamic
 demographic history that coincided with periods of climate variation
 during the Pleistocene. Overall, our study provides a clear example of how
 genomic data can uncover valuable insights into captive populations and
 contributes important resources to guide future management decisions of an
 endangered species.
description: Here we used whole genome resequencing data together with a
 chromosomal-level genome assembly to investigate diversity and
 demography in the scimitar-horned oryx, an extinct in the wild
 antelope. Illumina sequencing was carried out for six focal individuals at
 an average coverage of 15X. Raw sequencing reads were processed and mapped
 to the genome assembly for downstream analysis. This repository contains
 metadata and some processed files that should make it possible
 to reproduce our analyses using code available on github. Raw sequencing
 reads are stored in the European Nucleotide Archive (ENA) under study
 accession PRJEB37295. More information can be found in the README
 file.
description: Repositories containing the full analysis code can be found here:
 https://github.com/elhumble/SHO_reseq_2020 and here:
 https://github.com/elhumble/SHO_analysis_2020. The README file and
 comments in scripts should contain all relevant information to
 reproduce the downstream analyses in the paper.
DOI: 10.5061/dryad.4tmpg4f6p
title: Data from: Early-life exposure to artificial light at night elevates physiological stress in free-living songbirds

description: Artificial light at night (ALAN) can disrupt adaptive patterns of
 physiology and behavior that promote high fitness, resulting in
 physiological stress and elevation of steroid glucocorticoids
 (corticosterone, CORT in birds). Elevated CORT may have
 particularly profound effects early in life, with the potential for
 enduring effects that persist into adulthood. Research on the
 consequences of early-life exposure to ALAN remains limited,
 especially outside of the laboratory, and whether light exposure
 affects CORT concentrations in wild nestling birds
 particularly remains to be elucidated. We used an experimental
 setup to test the hypothesis that ALAN elevates
 CORT concentrations in developing free-living birds, by exposing
 nestling great tits (Parus major) to ALAN inside nest boxes. We
 measured CORT in feathers grown over the timeframe of the experiment (7
 nights), such that CORT concentrations represent an integrative
 metric of hormone release over the period of nocturnal light
 exposure, and of development. We also assessed the relationships
 between feather CORT concentrations, body condition, nestling
 size rank and fledging success. In addition, we evaluated the relationship
 between feather CORT concentrations and telomere length.
 Nestlings exposed to ALAN had higher feather CORT concentrations than
 control nestlings, and nestlings in poorer body condition and
 smaller brood members also had higher CORT. On the other hand,
 telomere length, fledging success, and recruitment rate were not
 significantly associated with light exposure or feather CORT
 concentrations. Results indicate that exposure to ALAN elevates CORT
 concentrations in nestlings, which may reflect physiological
 stress. In addition, the organizational effects of CORT are known to
 be substantial. Thus, despite the lack of an effect on telomere
 length and survivorship, elevated CORT concentrations in
 nestlings exposed to ALAN may have subsequent impacts on later-life
 fitness and stress sensitivity.
description: Nestling great tits (<em>Parus major</em>) were
 experimentally exposed to artificial light at night for 7 nights.  Blood
 samples were taken both before (day 8) and after (day 15) the light
 manipulation to assess telomere shortening and feather samples were taken
 on day 15 to measure corticosterone levels.  Feathers from which
 corticosterone levels were measured were grown over the timeframe of the
 experiment. Relative telomere length was measured using quantitative PCR
 and corticosterone was measured using standard radioimmunoassay
 techniques. Morphometric measurements (mass, tarsus length) were also
 taken on day 8 and15.
DOI: 10.5061/dryad.j9kd51c8q
title: Data from: Dietary antioxidants attenuate the endocrine stress response during long-duration flight of a migratory bird

description: Glucocorticoids (GCs) are metabolic hormones that promote catabolic
 processes, which release stored energy and support high metabolic demands
 such as during prolonged flights of migrating birds. Dietary antioxidants
 (e.g., anthocyanins) support metabolism by quenching excess reactive
 oxygen species produced during aerobic metabolism, and also by activating
 metabolic pathways that, similar to GCs’ function, release stored energy,
 although the extent of complementarity between GCs and dietary
 antioxidants is not well known. If anthocyanins complement GCs functions,
 birds consuming anthocyanin-rich food can be expected to limit the
 secretion of GCs when coping with a metabolically challenging activity,
 avoiding the exposure to potential hormonal detrimental effects. We tested
 this hypothesis in European starlings (Sturnus vulgaris) flying in a
 windtunnel. We compared levels of corticosterone, the main avian GCs,
 immediately after a sustained flight and at rest for birds that were fed
 diets with or without an anthocyanin supplement. As predicted, we found
 (1) higher corticosterone after flight than at rest in both diet groups,
 and (2) anthocyanin-supplemented birds had less elevated corticosterone
 after flight than unsupplemented control birds. This provides novel
 evidence that dietary antioxidants attenuate the activation of the HPA
 axis (i.e. increased secretion of corticosterone) during long-duration
 flight.
DOI: 10.5061/dryad.931zcrjh3
title: Data from: Ant collective behavior is heritable and shaped by selection

description: Collective behaviors are widespread in nature and usually assumed to be
 strongly shaped by natural selection. However, the degree to which
 variation in collective behavior is heritable and has fitness consequences
 -- the two prerequisites for evolution by natural selection -- is largely
 unknown. We used a new pharaoh ant ( Monomorium pharaonis ) mapping
 population to estimate the heritability, genetic correlations, and fitness
 consequences of three collective behaviors (foraging, aggression, and
 exploration) as well as body size, sex ratio, and caste ratio.
 Heritability estimates for the collective behaviors were moderate, ranging
 from 0.17 to 0.32, but lower than our estimates for the heritability of
 caste ratio, sex ratio, and the body size of new workers, queens, and
 males. Moreover, variation among colonies in collective behaviors was
 phenotypically correlated, suggesting that selection may shape multiple
 colony collective behaviors simultaneously. Finally, we found evidence for
 directional selection that was similar in strength to estimates of
 selection in natural populations. Altogether, our study begins to
 elucidate the genetic architecture of collective behavior and is one of
 the first studies to demonstrate that it is shaped by selection.