cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rv15dv47k
title: Subsampling and DNA pooling can increase gains through genomic selection in switchgrass

description: Genomic selection (GS) can accelerate breeding cycles in perennial crops
 such as the bioenergy grass switchgrass (Panicum virgatum L.).
 The sequencing costs of GS can be reduced by pooling DNA samples in the
 training population (TP), only sequencing TP phenotypic outliers, or
 pooling candidate population (CP) samples. These strategies were simulated
 for two traits (spring vigor and anthesis date) in three breeding
 populations. Sequencing only the outlier 50% of the TP phenotype
 distribution resulted in a penalty of &lt;5% of the predictive
 ability, measured using cross-validation. Predictive ability also
 decreased when sequencing progressively fewer TP DNA pools, but TPs
 constructed from only two phenotypically contrasting DNA samples retained
 a mean of &gt;80% predictive ability relative to individual TP
 sequencing. Novel group testing methods allowed greater than one CP
 individual to be screened per sequenced DNA sample but resulted in a
 predictive ability penalty. To determine the impact of reduced sequencing,
 genetic gain was calculated for seven GS scenarios with variable
 sequencing budgets. Reduced TP sequencing and most CP pooling methods were
 superior to individual sequence-based GS when sequencing resources were
 restricted (2,000 DNA samples per 5-yr cycle). Only one scenario was
 superior to individual sequencing when sequencing budgets were large
 (8,000 DNA samples per 5-yr cycle). This study highlights multiple routes
 for reduced sequencing costs in GS.
DOI: 10.5061/dryad.t1g1jwt1t
title: Stable isotope differences of polar bears in the Southern Beaufort Sea and Chukchi Sea

description: The life history, genetic, and habitat use differences between the 2 polar
 bear (Ursus maritimus) subpopulations in Alaska have been used to
 determine the geographic border separating them, but it has sparked a
 debate of the correct placement of the border for several years. Recently,
 the Southern Beaufort Sea (SBS) polar bear subpopulation has declined due
 to sea ice loss, while the Chukchi Sea (CS) subpopulation appears stable.
 To provide additional information about potential differences between the
 SBS and CS subpopulations, such as differences in prey sources, we used
 stable isotope analysis of carbon and nitrogen from bone collagen of polar
 bears in these 2 neighboring subpopulations.  We analyzed polar
 bear bones (1954–2019) from 112 individuals. Our purpose was to determine
 if the SBS and CS subpopulations could be distinguished based on the
 stable isotope signatures of bone collagen. A difference greater than 1‰
 in δ13C values suggests a change in carbon sources, such as nearshore to
 offshore, while a 3‰ change in δ15N values equates to a change of about 1
 trophic level. Our study showed a significant difference in δ13C values (P
 ≤ 0.001), but not δ15N values (P = 0.654) between the CS (−13.0±0.3‰ and
 22.0±0.9‰, respectively) and SBS bears (−14.7±1.3‰ and 22.2±1.0‰,
 respectively). Our findings indicate that the 2 subpopulations are
 consuming similar high trophic level prey, while feeding in ecosystems
 with different δ13C baselines. We performed a logistic regression analysis
 (LR) using δ13C and δ15N values of the polar bears to predict their
 placement into these 2 subpopulations. Using Icy Cape, AK as the
 geographical boundary, the LR correctly placed polar bears in their
 respective subpopulations 82% of the time. Overall accuracy of placement
 changed to 84% when using the current geographical boundary at Utqiaġvik,
 AK. Samples collected from the Wainwright, AK region were predicted as 58%
 CS and 42% SBS polar bears. This suggests that the area between Wainwright
 and Icy Cape is a polar bear mixing zone that includes bears from both
 subpopulations. Bone collagen has a long-term, potentially life-long,
 stable isotope turnover rate, and our findings could be used to determine
 the association of harvested polar bears to Alaska subpopulations, thus
 aiding in transboundary harvest quota management.
DOI: 10.5061/dryad.j3tx95xd0
title: Sex-specific genetic (co)variances of standard metabolic rate, body mass and locomotor activity in Drosophila melanogaster

description: A longstanding focus in evolutionary physiology concerns the causes and
 consequences of variation in maintenance metabolism. Insight into this can
 be gained by estimating the sex-specific genetic architecture of
 maintenance metabolism alongside other, potentially correlated traits on
 which selection may also act, such as body mass and locomotor activity.
 This may reveal potential genetic constraints affecting the evolution of
 maintenance metabolism. Here, we used a half-sibling breeding design to
 quantify the sex-specific patterns of genetic (co)variance in standard
 metabolic rate (SMR), body mass, and daily locomotor activity in
 Drosophila melanogaster. There was detectable additive genetic variance
 for all traits in both sexes. As expected, SMR and body mass were strongly
 and positively correlated, with genetic allometry exponents (bA±se) of
 0.66±0.16 in females and 0.58±0.32 in males. There was a significant and
 positive genetic correlation between SMR and locomotor activity in males,
 suggesting that alleles that increase locomotion have pleiotropic effects
 on SMR. Sexual differences in the genetic architecture were driven in
 large part by a difference in genetic variance in locomotor activity
 between the sexes. Overall, genetic variation was mostly shared between
 males and females, setting the stage for a potential intralocus sexual
 conflict in the face of sexually antagonistic selection.
description: see paper
DOI: 10.5061/dryad.wstqjq2kf
title: Pierce's disease vector transmission-preference experiment on PdR1 resistant grapevines

description: Host defense against vector-borne plant pathogens is a critical component
 of integrated disease management. However, theory predicts that traits
 that confer tolerance or partial resistance can, under certain ecological
 conditions, enhance the spread of pathogens and spillover to more
 susceptible populations or cultivars. A key component driving such
 epidemic risk appears to be variation in host selection behavior of
 vectors based on infection status of the host. While recent theory has
 further emphasized the importance of infection-induced host-selection
 behavior by insect vectors for plant disease epidemiology, experimental
 tests on the relationship between vector host-selection preference and
 transmission are lacking. We test how host plant defense—conferred by the
 PdR1 gene complex—mediates vector host-selection preference and
 transmission of the pathogenic bacterium Xylella fastidiosa among
 grapevine cultivars. We confirmed that PdR1 confers resistance against X.
 fastidiosa by reducing both pathogen population size and disease severity.
 We found that vector transmission rates to new hosts exhibited unimodal
 dynamics over the course of infection when both susceptible and resistant
 were infected and acted as sources of the pathogen. Transmission from
 susceptible plants initially increased and then declined as insect vectors
 avoided severely diseased plants. While transmission from PdR1 resistant
 plants also initially increased and then declined as well, this was not
 due to avoidance by vectors, although the exact mechanism remains unclear.
 We show that 1) vector preference changes over the course of disease
 progression, 2) vector preference is clearly important but a poor
 predictor of transmission, and 3) the post-latent incubation period—in
 which plant hosts are infectious but asymptomatic—is likely a key period
 for vector transmission of X. fastidiosa. Our results suggest that,
 consistent with theory, defensive traits lengthen the duration of the
 incubation period, increasing X. fastidiosa transmission. However,
 defensive traits may over the long-term ultimately reduce spread possibly
 through induced resistance. Vector host-selection preference, host
 resistance, and transmission are clearly dynamic, changing over the course
 of disease progression. Understanding these dynamics is critical for
 broader insights into the epidemiology of vector-borne plant pathogens,
 theory development, and deploying disease resistant cultivars in an
 effective and sustainable manner.
DOI: 10.5061/dryad.2rbnzs7mz
title: Seasonal distributions and predicting migratory pathways for three species of bats

description: Understanding seasonal variation in the distribution and movement patterns
 of migratory species is essential to monitoring and conservation efforts.
 While there are many species of migratory bats in North America, little is
 known about their seasonal movements. In terms of conservation, this is
 important because the bat fatalities from wind energy turbines are
 significant and may fluctuate seasonally. Here we describe seasonally
 resolved distributions for the three species that are most impacted by
 wind farms (Lasiurus borealis [eastern red bat], L. cinereus [hoary bat],
 and Lasionycteris noctivagans [silver-haired bat]) and use these
 distributions to infer their most likely migratory pathways. To accomplish
 this, we collected 2880 occurrence points from the Global Biodiversity
 Information Facility over five decades in North America to model species
 distributions on a seasonal basis and used an ensemble approach for
 modeling distributions. This dataset included 1,129 data points for L.
 borealis, 917 for L. cinereus, and 834 for L. noctivagans. The results
 suggest that all three species exhibit variation in distributions from
 north to south depending on season, with each species showing potential
 migratory pathways during the fall migration that follow linear features.
  Finally, we describe proposed migratory pathways for these three
 species that can be used to identify stop-over sites, assess small-scale
 migration and highlight areas that should be prioritized for actions to
 reduce the effects of wind farm mortality.
DOI: 10.5061/dryad.3r2280gfh
title: Data from: Free-energy changes of bacteriorhodopsin point mutants measured by single-molecule force spectroscopy

description: Single-amino-acid mutations provide quantitative insight into the
 energetics that underlie the dynamics and folding of membrane proteins.
 Chemical denaturation is the most widely used assay and yields the change
 in unfolding free energy (ΔΔG). It has been applied to &gt;80
 different residues of bacteriorhodopsin (bR), a model membrane protein.
 However, such experiments have several key limitations: (i) a non-native
 lipid environment, (ii) a denatured state with significant secondary
 structure, (iii) error introduced by extrapolation to zero denaturant, and
 (iv) the requirement of globally reversible refolding. We overcame these
 limitations by reversibly unfolding local regions of an individual protein
 with mechanical force using an atomic-force-microscope assay optimized for
 2-ms time resolution and 1-pN force stability. In this assay, bR was
 unfolded from its native bilayer into a well-defined, stretched state. To
 measure ΔΔG, we introduced two alanine point mutations into an
 8-amino-acid region at the C-terminal end of bR’s G helix. For each, we
 reversibly unfolded and refolded this region hundreds of times while the
 rest of the protein remained folded. Our single-molecule-derived ΔΔG for
 mutant L223A (−2.3 ± 0.6 kcal/mol) quantitatively agreed with past
 chemical-denaturation results while our ΔΔG for mutant V217A was 2.2-fold
 larger (−2.4 ± 0.6 kcal/mol). We attribute the latter result, in part, to
 contact between Val217 and a natively bound squalene lipid, highlighting
 the contribution of membrane-protein–lipid contacts not present in
 chemical-denaturation assays. More generally, we established a platform
 for determining ΔΔG for a fully folded membrane protein embedded in its
 native bilayer.
description: All data are comma delimited and in SI units. Data shown in each
 figure in the paper or SI Appendix are saved as separate files in this
 repository. Force-spectroscopy data are saved in the form of force versus
 either time or molecular extension ("ext"). Rate map data are
 denoted by molecular transition; e.g,. k_01 is the rate for the transition
 from state 0 to state 1. Uncertainties in these rates are saved as, e.g.,
 dk_01. These rates are to be plotted versus force_data. Rates evaluated
 from Bell-model fits are denoted, e.g., fitBE_01, to be plotted versus
 force_fitBE. Image data are stored as two-dimensional arrays of numerical
 values, each of which is a height.
DOI: 10.5061/dryad.3n5tb2rgm
title: Genomic evidence that governmentally produced Cannabis sativa poorly represents genetic variation available in state markets

description: The National Institute on Drug Abuse (NIDA) is the sole producer of
 Cannabis for research purposes in the United States, including medical
 investigation. Previous research established that cannabinoid profiles in
 the NIDA varieties lacked diversity and potency relative to the Cannabis
 produced commercially. Additionally, microsatellite marker analyses have
 established that the NIDA varieties are genetically divergent form
 varieties produced in the private legal market. Here, we analyzed the
 genome of multiple Cannabis varieties from diverse lineages including two
 produced by NIDA, and we provide further support that NIDA’s varieties
 differ from widely available medical, recreational, or industrial
 Cannabis. Furthermore, our results suggest that NIDA’s varieties lack
 diversity in the single copy portion of the genome, the maternally
 inherited genomes, the cannabinoid genes, and in the repetitive content of
 the genome. Therefore, results based on NIDA’s varieties are not
 generalizable regarding the effects of Cannabis after consumption. For
 medical research to be relevant, material that is more widely used would
 have to be studied. Clearly, having research to date dominated by a
 single, non-representative source of Cannabis has hindered scientific
 investigation.
DOI: 10.5061/dryad.pc866t1nf
title: Population genomics and conservation management of a declining tropical rodent

description: Conservation management is improved by incorporating information about the
 spatial distribution of population genetic diversity into planning
 strategies. Northern Australia is the location of some of the world’s most
 severe ongoing declines of endemic mammal species, yet we have little
 genetic information from this regional mammal assemblage to inform a
 genetic perspective on conservation assessment and planning. We used
 next-generation sequencing data from remnant populations of the threatened
 brush-tailed rabbit-rat (Conilurus penicillatus) to compare patterns of
 genomic diversity and differentiation across the landscape and investigate
 standardised hierarchical genomic diversity metrics to better understand
 brush-tailed rabbit-rat population genomic structure. We found strong
 population structuring, with high levels of differentiation between
 populations (FST = 0.21 to 0.78). Two distinct genomic lineages between
 the Tiwi Islands and mainland are also present. Prioritisation analysis
 showed that one population in both lineages would need to be conserved to
 retain at least ~80% of alleles for the species. Analysis of standardised
 genomic diversity metrics showed that approximately half of the total
 diversity occurs among lineages (? = 0.091 from grand total γ = 0.184). We
 suggest that a focus on conserving remnant island populations may not be
 appropriate for the preservation of species-level genomic diversity and
 adaptive potential, as these populations represent a small component of
 the total diversity and a narrow subset of the environmental conditions in
 which the species occurs. We also highlight the importance of considering
 both genomic and ecological differentiation between source and receiving
 populations when considering translocations for conservation purposes.
description: We used next-generation sequencing data from remnant populations
 of the threatened brush-tailed rabbit-rat (<i>Conilurus
 penicillatus</i>) to compare patterns of genomic diversity and
 differentiation across the landscape and investigate standardised
 hierarchical genomic diversity metrics to better understand brush-tailed
 rabbit-rat population genomic structure. All
 bioinformatic and R scripts are provided as part of the dataset. ANGSD
 output and filtered genotypes are provided in separate folders, as well as
 rasters used in hypervolume calculations.
DOI: 10.5061/dryad.pvmcvdnkb
title: Nutrient trade-offs mediated by ectomycorrhizal strategies in plants: Evidence from an Abies species in subalpine forest

description: 1.    Ectomycorrhizal (ECM) symbiosis
 is an evolutionary biological trait of higher plants for effective
 nutrient uptakes. However, little is known that how the formation and
 morphological differentiations of ECM roots mediate the nutrients of
 below- and aboveground plant tissues and the balance among nutrient
 elements across environmental gradients. Here we investigated the effects
 of ECM foraging strategies on root and foliar N and P concentrations and
 N:P ratio Abies faxoniana under variations of climate and soil conditions.
 2.    The ECM symbionts preferentially
 mediated P uptake under both N and P limitations. The uptake efficiency of
 N and P was primarily associated with the ECM root traits, e.g., ECM root
 tip density, superficial area of ECM root tips, the ratio of living to
 dead root tips, and was affected by the ECM proliferations and
 morphological differentiations. The tissue N and P concentrations were
 positively associated with the abundance of the contact exploration type,
 and negatively with that of the short-distance exploration type.
 3.    Our findings indicate that the
 nutritional status of both below- and aboveground plant tissues can be
 strongly affected by ECM symbiosis in natural environments. Variations in
 the ECM strategies in response to varying environmental conditions
 significantly influence plant nutrient uptakes and trade-offs.
description: Root and soil samples were collected during June-August, 2018, at
 five elevations (2850, 3000, 3194, 3413, and 3593 m asl.) in Wolong Nature
 Reserve, and two elevations in Miyaluo Nature Reserve (3077 and 3612 m
 asl.) and Wanglang Nature Reserve (3070 and 3150 m asl.), respectively,
 using point-centered quarter sampling method with randomly selected mature
 A. faxoniana trees (n = 8 focal trees per site) as center points. We
 collected fully developed, current year leaves from each target tree
 evenly at northern, eastern, southern, and western directions and among
 the four target trees at each center point. we identified key soil
 variables and ECM traits by principal component analysis (PCA), and the
 first and second principal components of soil variables (named Soil-PC1,
 Soil-PC2 respectively) and ECM traits (named ECM-PC1, ECM-PC2
 respectively) were selected for SEMs analyses.  The
 gridded daily climate dataset (CN05.1), with a spatial resolution of
 0.25<sup>°</sup>×0.25<sup>° </sup>constructed by
 the “anomaly approach” during the interpolation with more 2400 station
 observations in China, was employed to obtain the meteorological data for
 the study sites during 1997-2016. The mean annual temperature (MAT, ℃) for
 each elevation on each site was derived through topographic correction
 with the lapse rate of air temperature set at
 0.65<sup>◦</sup>C (100 m)<sup>-1</sup>. The same
 value of the mean annual precipitation (MAP, mm) was assumed along the
 elevational gradient on each site.
DOI: 10.5061/dryad.h70rxwdht
title: Quantity discrimination in a lizard

description: While foraging or during social interactions, animals may benefit from
 judging relative quantity. Individuals may select larger prey or a patch
 with more food and likewise, it may pay to track the number and type of
 individuals and social interactions. We tested for spontaneous quantity
 discrimination in the gidgee skink (Egernia stokesii), a family-living
 lizard. Lizards were presented with food quantities differing in number or
 size and selected the larger quantity of food items when they differed in
 number, but not when items differed in size. We show, for the first time,
 superior spontaneous discrimination of items differing in number over size
 in a lizard species which contrasts with previous findings. Our simple
 method, however, did not include controls for the use of continuous
 quantities and further tests are required to determine the role of such
 information during quantity discrimination. Our results provide support
 for use of the parallel individuation system for the discrimination of
 small quantities (£ 4 items). Lizards might, however, still use the
 approximate number system if items in larger quantities (&gt; 4) are
 presented. Overall, we uncovered evidence that species might possess
 specific cognitive abilities potentially adapted to their niche in respect
 to quantity information (discrete and/or continuous) and the processing
 system used when judging quantities. Importantly, our results highlight
 the need for testing multiple species using similar testing procedures to
 gain a better understanding of the underlying causes leading to
 differences across species.
description: Data were collected during a spontanious two choice quantity
 discrimination task. Lizards were presented with two options of quantities
 (number of food items and differently sized food items) and their first
 choice was recorded. Lizards were not rewarded for choices to prevent
 learning. All data manipulation is done in R. The provided data set
 represents the most raw unchanged form of the collected data.
description: A read me data file is provided which explains every variable in
 the dataset.