cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rr4xgxd9c
title: Island biogeography theory and the urban landscape: stopover site selection by the silver-haired bat (Lasionycteris noctivagans)

description: Many migratory bats require forested sites for roosting and foraging along
 their migration path, but increased urbanization and intensive
 agricultural practices may reduce the availability of stopover sites.
 Urban forests may provide important stopover habitat, maintaining
 landscape connectivity in regions where the majority of natural habitat
 has been cleared for development. Island biogeography theory can be
 applied to urbanized temperate forest biomes where small urban forests
 represent islands separated from the larger “mainland” forest. We used
 acoustic monitoring during the fall migration period to investigate the
 use of urban forest habitat by the migratory species Lasionycteris
 noctivagans (Le Conte 1831). We predicted that recorded activity would
 have a positive relationship with forest patch area and shape and a
 negative relationship with isolation from other forest patches, as
 suggested by island biogeography theory. We observed greater activity at
 larger forest patches, and although relationships for shape and isolation
 were not statistically supported the observed patterns were consistent
 with predictions. Our results demonstrate the need for more in-depth
 research on the habitat requirements for both migratory and resident bat
 species and the impact that ongoing urbanization has on local bat
 populations.
DOI: 10.5061/dryad.t76hdr828
title: Frequent paternal mitochondrial inheritance and rapid haplotype frequency shifts in copepod hybrids

description: Mitochondria are assumed to be maternally inherited in most animal
 species, and this foundational concept has fostered advances in
 phylogenetics, conservation, and population genetics. Like other animals,
 mitochondria were thought to be solely maternally inherited in the marine
 copepod Tigriopus californicus, which has served as a
 useful model for studying mitonuclear interactions, hybrid breakdown, and
 environmental tolerance. However, we present PCR, Sanger sequencing, and
 Illumina Nextera sequencing evidence that extensive paternal mitochondrial
 DNA (mtDNA) transmission is occurring in inter-population hybrids
 of T. californicus. PCR on four types of crosses between three
 populations (total sample size of 376 F1 individuals) with 20%
 genome-wide mitochondrial divergence showed 2% to 59% of F1 hybrids with
 both paternal and maternal mtDNA, where low and high paternal leakage
 values were found in different cross directions of the same population
 pairs. Sequencing methods further verified nucleotide similarities between
 F1 mtDNA and paternal mtDNA sequences. Interestingly, the paternal mtDNA
 in F1s from some crosses inherited haplotypes that were uncommon in the
 paternal population. Compared to some previous research on
 paternal leakage, we employed more rigorous methods to rule out
 contamination and false detection of paternal mtDNA due to non-functional
 nuclear mitochondrial DNA fragments. Our results raise the
 potential that other animal systems thought to only inherit maternal
 mitochondria may also have paternal leakage, which would then affect the
 interpretation of past and future population genetics or phylogenetic
 studies that rely on mitochondria as uniparental markers.
description: ABscaffolds_trim.fasta: This file contains a genome assembly made
 with SPADES
DOI: 10.5061/dryad.73n5tb2z5
title: Functionally dissimilar neighbors improve tree water use efficiency through increases in leaf phosphorus concentration

description: Water use efficiency (WUE) is central to the global cycles of water and
 carbon. However, whether increasing tree diversity in plantation can
 increase WUE remain poorly understood. Here, we conduct a forest
 biodiversity experiment with 32 tree species spread in 14 ha in
 subtropical China to assess the effects of neighboring tree diversity on
 foliar WUE of Cunninghamia lanceolata, a widespread tree plantation
 species in China. We measure foliar δ13C as the proxies of changes in
 intrinsic WUE. Folia P concentrations of focal trees increase with trait
 dissimilarities between focal trees and neighbors, and the increased
 foliar P concentrations improve foliar WUE of focal trees. This
 neighborhood complementarity effect on WUE is stronger under more shaded
 neighborhood. However, neighborhood biodiversity did not significantly
 affect foliar δ18O, a surrogate for stomatal
 conductance. These findings suggest that tree biodiversity increases WUE
 through the complementary usages of soil P between neighboring tree
 species.
DOI: 10.5061/dryad.c59zw3r8k
title: Data from: Loss of fungal symbionts at the arid limit of the distribution range in a native Patagonian grass – resource ecophysiological relations

description: 1. Crucial to our understanding of plant ecology is the consideration of
 the eco-physiological responses and constraints of plant-fungal symbioses
 throughout the native distribution range of their host. 2. We
 examined key eco-physiological roles of two co-occurring fungal symbionts
 [Epichloë endophytes and arbuscular mycorrhizal fungi (AMF)] in the
 endemic grass Hordeum comosum across a wide bioclimatic gradient and
 contrasting grazing severity. We sampled H. comosum plants along four
 humid-to-arid transects in Patagonia, Argentina, covering its entire
 distribution range and determined Epichloë presence, AMF root
 colonization, nitrogen and phosphorus concentration, intrinsic water
 use-efficiency (iWUE, the ratio of photosynthesis to stomatal conductance)
 and 18O-enrichment of cellulose in shoots. 3. Root colonization by AMF
 increased with Epichloë-presence. All plants hosted Epichloë in the humid
 range of the gradient, but symbioses occurrence decreased towards arid
 sites which also displayed severe grazing symptoms at site level. 4.
 Symbiosis with Epichloë correlated positively with shoot nitrogen
 concentration in the centre of the distribution range, and with shoot
 phosphorus concentration across the entire distribution range.
 5. The site-level relationship of AMF colonization with
 18O-enrichment and iWUE suggested that mycorrhiza boosted stomatal
 conductance in humid environments but curbed it in arid environments.
 6. While the interpretation of interactions and potential
 causalities from observational studies should be done with caution, this
 study demonstrates distinct correlations between plant-fungal symbiont
 associations and key resource parameters (phosphorus, nitrogen, and iWUE
 vs 18O-enrichment). Such correlations may suggest particular functional
 roles for these symbionts in the ecology of their host plant.
DOI: 10.5061/dryad.66t1g1k39
title: Sea surface temperature and habitat effects on juvenile reef fish communities along a tropicalising coastline

description: Aim: Temperate marine systems globally are warming at accelerating rates,
 facilitating the poleward movement of warm-water species which are
 tropicalising higher-latitude reefs. While temperature plays a key role in
 structuring species distributions, less is known about how species'
 early life stages are responding to warming-induced changes in preferred
 nursery habitat availability. We aim to identify the key ecological and
 environmental drivers of juvenile reef fishes' distributions in the
 context of ocean warming. Location: South-eastern Australian coastline
 from 30-37°S. Methods: We used a decade of underwater visual census data
 to uncover latitudinal distribution patterns of juvenile reef fishes and
 habitats across 1,000 km of coastline, from subtropical to temperate
 latitudes. We modelled how benthic habitat cover, depth, wave exposure and
 sea surface temperature influence distributions of warm-water and
 cool-water juvenile reef fishes on temperate rocky reefs. Results: We
 found sea surface temperature was typically the most important factor
 influencing densities of juvenile fishes, regardless of species thermal
 affinity or latitudinal range extent. Tropical and subtropical
 range-expanding fishes responded more strongly to warmer temperatures than
 temperate species, whose juveniles displayed stronger habitat
 associations. Species' responses to greater availability of temperate
 reef habitat-formers such as kelp and other macroalgae contrasted, being
 positive for temperate and negative for tropical and subtropical juvenile
 fishes. Main conclusions: The availability of both suitable habitat and
 thermal niches for species' early life stages are important
 considerations when predicting changes in reef fishes' distributions
 in the context of ocean warming. Warming-induced isotherm shifts and
 feedback loops constraining the persistence of key temperate reef
 habitat-formers will favour range-expanding tropical reef fishes
 colonising higher-latitude reefs, while disadvantaging some
 habitat-associated resident temperate species. Species' varying
 responses to warming-induced environmental changes will strongly influence
 the structure of emerging tropicalised reef assemblages.
description: Dataset used for analyses
DOI: 10.5061/dryad.mcvdnck29
title: Phenotypic and Genetic data for "Evolution of fruit and seed traits during almond naturalization"

description: 1- Cultivated plant species often naturalize and enter wild communities in
 a process known as feralization. To successfully feralize, crops must
 overcome ecological barriers and may undergo selection on certain traits,
 diverging phenotypically and genetically from their crop ancestors. In
 spite of the agronomic and ecological relevance of crop feralization, the
 eco-evolutionary dynamics driving it remain understudied. 2- In this
 paper, we evaluated phenotypic and genotypic differentiation in fruit and
 seed traits during the naturalization of the almond tree (Prunus dulcis
 (Mill.) D.A. Webb) in SE Iberia and evaluated the potential role of
 natural selection in this process. To do so, we investigated patterns of
 genetic divergence between cultivated and feral populations using
 functional (the cyanogenesis Sk gene) and neutral (17 SSR loci) markers
 and analyzed morphological and biochemical traits in kernels of 342
 individuals from 15 cultivated and 24 feral populations. 3- We detected
 very little genetic differentiation in neutral markers between cultivated
 and feral populations. The majority of the observed genetic variation was
 due to differences within each type. Conversely, the recessive allele sk
 responsible for seed toxicity was significantly more frequent in feral
 populations. Phenotypic differentiation between cultivated and naturalized
 almond populations was also significant. Feral almond kernels were smaller
 and lighter, had denser and more resistant shells (endocarps) and more
 toxic seeds. Selection analyses indicated that these genetic and
 phenotypic patterns might be driven by directional selection on fruit and
 seed traits, potentially linked to defense against predation. 4-
 Synthesis. Our findings indicate that almond naturalization is consistent
 with strong directional selection on fruits and seeds, leading to smaller
 and more toxic seeds encased in harder endocarps. Accordingly, we propose
 that feralization of this crop is, at least to some degree, driven by
 adaptive evolution of dispersal and recruitment traits.
description: Usage note indicated in the Readme file (README.txt)
DOI: 10.34740/kaggle/dsv/14647870
title: Forex Exchange Rates Since 2004 (Updated Daily)
DOI: 10.26165/juelich-data/mzsjbn
title: quinex

description: quinex (quantitative information extraction) is a Python library for extracting and analyzing quantitative information from text. It is designed to extract quantities, entities, properties and other measurement context from text. Quinex is domain-agnostic and can power a wide range of applications, such as screening of scientific literature or quantitative search.
DOI: 10.5061/dryad.573n5tb8s
title: Data from: Sharing detection heterogeneity information among species in community models of occupancy and abundance can strengthen inference

description: 1. The estimation of abundance and distribution and factors governing
 patterns in these parameters is central to the field of
 ecology. The continued development of hierarchical models that
 best utilize available information to inform these processes is a key goal
 of quantitative ecologists. However, much remains to be learned
 about simultaneously modeling true abundance, presence, and trajectories
 of ecological communities. 2. Simultaneous modeling of the
 population dynamics of multiple species provides an interesting mechanism
 to examine patterns in community processes and, as we emphasize
 herein, to improve species-specific estimates by leveraging detection
 information among species. Here we demonstrate a simple but
 effective approach to share information about observation parameters among
 species in hierarchical community abundance and occupancy
 models, where we use shared random effects among species to
 account for spatiotemporal heterogeneity in detection probability.
 3. We demonstrate the efficacy of our modeling approach using
 simulated abundance data, where we recover well our simulated parameters
 using N-mixture models. Our approach substantially increases
 precision in estimates of abundance compared to models that do not share
 detection information among species. We then expand this model,
 and apply it to repeated detection/non-detection data collected on six
 species of tits (Paridae) breeding at 119 1 km2 sampling
 sites across a P. montanus hybrid zone in northern Switzerland
 (2004-2020). We find strong impacts of forest cover and elevation
 on population persistence and colonisation in all species. We
 also demonstrate evidence for interspecific competition on population
 persistence and colonization probabilities, where the presence of
 marsh tits reduces population persistence and colonisation
 probability of sympatric willow tits, potentially decreasing gene
 flow among willow tit subspecies. 4. While conceptually simple, our
 results have important implications for the future modeling of population
 abundance, colonization, persistence, and trajectories in
 community frameworks. We suggest potential extensions of our modeling in
 this paper, and discuss how leveraging data from multiple species
 can improve model performance and sharpen ecological inference.
DOI: 10.5061/dryad.nvx0k6dtk
title: Arabidopsis Glutathione-S-Transferases GSTF11 and GSTU20 function in Aliphatic Glucosinolate Biosynthesis

description: GSH conjugation with intermediates is required for the biosynthesis of
 glucosinolate (GSL) by serving as a sulfur supply.
 Glutathione-S-transferases (GSTs) primarily work on GSH conjugation,
 suggesting their involvement in GSL metabolism. Although several GSTs,
 including GSTF11 and GSTU20, have been recently postulated to act in GSL
 biosynthesis, molecular evidence is lacking. Here, we demonstrated that
 GSTF11 and GSTU20 play nonredundant, although partially overlapping, roles
 in aliphatic GSL biosynthesis. In addition, GSTU20 plays a more important
 role than GSTF11, which is manifested by the greater loss of aliphatic
 GSLs associated with GSTU20 mutant and a greater number of differentially
 expressed genes in GSTU20 mutant compared to GSTF11 mutant. Moreover, a
 double mutation leads to a greater aggregate loss of aliphatic GSLs,
 suggesting that GSTU20 and GSTF11 may function in GSL biosynthesis in a
 dosage-dependent manner. Together, our results provide direct evidence
 that GSTU20 and GSTF11 are critically involved in aliphatic GSL
 biosynthesis, filling the knowledge gap that has been speculated in recent
 decades.
description: Total RNA was extracted from three-week-old plants with TRIzol
 (Invitrogen) and purified using a GeneJET plant RNA purification kit
 (Thermo Fisher Scientific). RNA integrity and concentration were assessed
 by gel electrophoresis and using the Qubit® 2.0 Fluorometer (Thermo Fisher
 Scientific). RNA (1.5 μg) was used for cDNA library preparation with the
 NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs,
 NEB) following the manufacturer’s protocol. Library quality was monitored
 using an Agilent Bioanalyzer 2100 (Agilent Technologies). The cDNA
 libraries were sequenced on an Illumina HiSeq 2500 platform, and 150-bp
 paired-end reads were generated. Gene functional
 annotation was conducted by aligning reads to the Arabidopsis genome
 sequence (TAIR 10). Following alignment, the count of mapped reads from
 each sample was derived and normalized as RPKM (reads per kilobase of exon
 model per million mapped reads). Differentially expressed genes (DEGs)
 were identified using the DESeq R package (1.10.1). Genes with log2 fold
 change ≥ 1 and an FDR adjusted <i>p </i>value less than 0.05
 were considered DEGs. GO term enrichment of DEGs was analyzed using tools
 in TAIR.
DOI: 10.5061/dryad.dr7sqvb0g
title: Root traits reveal safety and efficiency differences in grasses and shrubs exposed to different fire regimes

description: Roots are key components of terrestrial ecosystems, yet little is known
 about how root structure and function vary across a broad range of
 species, functional groups, and ecological gradients in situ. We assessed
 how woody and grass root anatomical traits vary among soil depths and
 different fire frequencies to better understand the water-use strategies
 exhibited by these two functional groups in tallgrass prairie experiencing
 woody encroachment. Specifically, we asked: (1) Do root anatomical traits
 differ with fire frequency or soil depth? (2) Do relationships between
 anatomical traits that confer hydraulic safety versus efficiency vary by
 fire frequency or soil depth? (3) Is root anatomy associated with
 integrative root traits (e.g., root diameter, specific root length (SRL),
 and root biomass)? (4) When scaled by root biomass, do root water-use
 traits impact the capacity for water uptake? We collected grass and woody
 roots from 10, 30, and 50 cm deep soil in areas burned every 1, 4, and
 20-years. We then measured xylem conduit diameter, conduit cell wall
 thickness, conduit number, conduit mechanical safety (t/b), stele area,
 endoderm thickness, hydraulic diameter, theoretical hydraulic
 conductivity, and root-system theoretical hydraulic conductance. We
 observed: (1) Woody roots had high hydraulic conductance in shallow soils
 and greater mechanical strength in deeper soils, which may provide a
 competitive advantage in less frequently burned, more diverse plant
 communities; (2) Shallow grass roots had unique trait combinations at the
 anatomical and root-system levels (thinner, more numerous conduits and
 higher root-system hydraulic conductance compared to deeper roots) that
 likely allow these plants to rapidly use water but tolerate dry soils
 under multiple fire regimes; and (3) hydraulic safety versus efficiency
 tradeoffs translate between different hierarchical scales (i.e., from
 anatomical to integrative root traits). These results provide anatomical
 evidence to explain water-use dynamics in tallgrass prairie and also
 provide novel insight regarding functional strategies that may facilitate
 the conversion from grassland to shrubland in less frequently burned
 tallgrass prairie. Future work should investigate these dynamics in situ,
 as they may explain current and future patterns of woody-grass coexistence
 in tallgrass prairies.
DOI: 10.5061/dryad.3bk3j9km2
title: Data from: Gobbling across landscapes: Eastern wild turkey distribution and occupancy-habitat associations

description: Extensive restoration and translocation efforts beginning in the mid-20th
 century helped to reestablish eastern wild turkeys (Meleagris gallopavo
 silvestris) throughout their ancestral range.  The adaptability
 of wild turkeys resulted in further population expansion in regions that
 were considered unfavorable during initial reintroductions across the
 northern United States.  Identification and understanding of
 species distributions and contemporary habitat associations are important
 for guiding effective conservation and management strategies across
 different ecological landscapes.  To investigate differences in
 wild turkey distribution across two contrasting regions, heavily forested
 northern Wisconsin, USA, and predominately agricultural southeast
 Wisconsin, we conducted 3,050 gobbling call-count surveys from March–May
 2014–2018 and used multiseason correlated-replicate occupancy models to
 evaluate occupancy-habitat associations and distributions of wild turkeys
 in each study region.  Detection probabilities varied widely and
 were influenced by sampling period, time of day, and wind speed. 
 Spatial autocorrelation between successive stations was prevalent along
 survey routes but were stronger in our northern study area.  In
 heavily forested northern Wisconsin, turkeys were more likely to occupy
 areas characterized by moderate availability of open land cover.
  Conversely, large agricultural fields decreased the likelihood
 of turkey occupancy in southeast Wisconsin, but occupancy probability
 increased as upland hardwood forest cover became more aggregated on the
 landscape.  Turkeys in northern Wisconsin were more likely to
 occupy landscapes with less snow cover and a higher percentage of row
 crops planted in corn.  However, we were unable to find
 supporting evidence in either study area that abandonment of turkeys from
 survey routes was associated with snow depth or with the percentage of
 agricultural cover.  Spatially, model-predicted estimates of
 patch-specific occupancy indicated turkey distribution was nonuniform
 across northern and southeast Wisconsin.  Our findings
 demonstrate that the environmental constraints of turkey occupancy varied
 across the latitudinal gradient of the state with open cover, snow, and
 row crops being influential in the north, and agricultural areas and
 hardwood forest cover important in the southeast.  These forces
 contribute to non-stationarity in wild turkey-environmental relationships.
  Key habitat-occupancy associations identified in our results can
 be used to prioritize and strategically target management efforts and
 resources in areas that are more likely to harbor sustainable turkey
 populations.
description: Variables in PRESENCE input files have been standardized.
DOI: 10.5061/dryad.h70rxwdkk
title: Extraordinarily precise nematode sex ratios: adaptive responses to vanishingly rare mating opportunities

description: Sex ratio theory predicts both mean sex ratio and variance under a range
 of population structures. Here, we compare two genera of phoretic
 nematodes (Parasitodiplogaster and Ficophagus spp.) associated with twelve
 fig-pollinating wasp species in Panama. The host wasps exhibit classic
 Local Mate Competition: only inseminated females disperse from natal figs,
 and their offspring form mating pools that consist of scores of the adult
 offspring contributed by one or a few foundress mothers. In contrast, in
 both nematode genera only sexually undifferentiated juveniles disperse and
 their mating pools routinely consist of ten or fewer adults. Across all
 mating pool sizes, the sex ratios observed in both nematode genera are
 consistently female-biased (~0.34 males), which is markedly less
 female-biased than is often observed in the host wasps (~0.10 males). In
 further contrast with their hosts, variances in nematode sex ratios are
 also consistently precise (significantly less than binomial). The
 constraints associated with predictably small mating pools within highly
 subdivided populations appear to select for precise sex ratios that
 contribute both to the reproductive success of individual nematodes, and
 to the evolutionary persistence of nematode species. We suggest that some
 form of environmental sex determination underlies these precise sex
 ratios.