cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mkkwh7142
title: Data from: A case for the “Competitive exclusion – tolerance rule” as a general cause of species turnover along environmental gradients

description: Closely-related, ecologically-similar species often segregate their
 distributions along environmental gradients of time, space, and resources,
 but previous research suggests diverse underlying causes. Here, we review
 reciprocal removal studies in nature that experimentally test the role of
 interactions among species in determining their turnover along
 environmental gradients. We find consistent evidence for asymmetric
 exclusion coupled with differences in environmental tolerance causing the
 segregation of species pairs, where a dominant species excludes a
 subordinate from benign regions of the gradient, but is unable to tolerate
 challenging regions to which the subordinate species is adapted.
 Subordinate species were consistently smaller and performed better in
 regions of the gradient typically occupied by the dominant species
 compared to their native distribution. These results extend previous ideas
 contrasting competitive ability with adaptation to abiotic stress to
 include a broader diversity of species interactions (intraguild predation,
 reproductive interference) and environmental gradients, including
 gradients of biotic challenge. Collectively, these findings suggest that
 adaptation to environmental challenge compromises performance in
 antagonistic interactions with ecologically-similar species. The
 consistency of this pattern across diverse organisms, environments, and
 biomes suggests generalizable processes structuring the segregation of
 ecologically-similar species along disparate environmental gradients, a
 phenomenon that we propose should be named the Competitive exclusion –
 tolerance rule.
description: Literature review and
 meta-analysis. Please see Methods of paper.
description: Includes R
 script.
DOI: 10.5061/dryad.w6m905qsw
title: Evaluating drivers of female dominance in the spotted hyena: R code and data

description: Introduction: Dominance relationships in which females dominate males are
 rare among mammals. Mechanistic hypotheses explaining the occurrence of
 female dominance suggest that females dominate males because 1) they are
 intrinsically more aggressive or less submissive than males, and/or 2)
 they have access to more social support than males. Methods: Here, we
 examine the determinants of female dominance across ontogenetic
 development in spotted hyenas (Crocuta crocuta) using 30 years of detailed
 behavioral observations from the Mara Hyena Project to evaluate these two
 hypotheses. Results: Among adult hyenas, we find that females
 spontaneously aggress at higher rates than males, whereas males
 spontaneously submit at higher rates than females. Once an aggressive
 interaction has been initiated, adult females are more likely than
 immigrant males to elicit submission from members of the opposite sex, and
 both adult natal and immigrant males are more likely than adult females to
 offer submission in response to an aggressive act. We also find that adult
 male aggressors are more likely to receive social support than adult
 female aggressors, and that both adult natal and immigrant males are 2-3
 times more likely to receive support when attacking a female than when
 attacking another male. Across all age classes, females are more likely
 than males to be targets of aggressive acts that occur with support.
 Further, receiving social support does slightly help immigrant males
 elicit submission from adult females compared to immigrant males acting
 alone, and it also helps females elicit submission from other females.
 However, adult females can dominate immigrant males with or without
 support far more often than immigrant males can dominate females, even
 when the immigrants are supported against females. Discussion: Overall, we
 find evidence for both mechanisms hypothesized to mediate female dominance
 in this species: 1) male and female hyenas clearly differ in their
 aggressive and submissive tendencies, and 2) realized social support plays
 an important role in shaping dominance relationships within a clan.
 Nevertheless, our results suggest that social support alone cannot explain
 sex-biased dominance in spotted hyenas. Although realized social support
 can certainly influence fight outcomes among females, adult females can
 easily dominate immigrant males without any support at all.
description: Use of data requires R software and R Studio software.
DOI: 10.5061/dryad.tqjq2bw3g
title: Spring and latch dynamics can act as control pathways in ultrafast systems

description: Ultrafast movements propelled by springs and released by latches are
 thought limited to energetic adjustments prior to movement and seemingly
 cannot adjust once movement begins. Even so, across the tree of life,
 ultrafast organisms navigate dynamic environments and generate a range of
 movements, suggesting unrecognized capabilities for control. We develop a
 framework of control pathways leveraging the non-linear dynamics of
 spring-propelled, latch-released systems. We analytically model spring
 dynamics and develop reduced-parameter models of latch dynamics to
 quantify how they can be tuned internally or through changing external
 environments.  Using Lagrangian mechanics, we test feedforward
 and feedback control implementation via spring and latch dynamics. We
 establish through empirically-informed modeling that ultrafast movement
 can be controllably varied during latch release and spring propulsion. A
 deeper understanding of the interconnection between multiple control
 pathways, and the tunability of each control pathway, in ultrafast
 biomechanical systems presented here has the potential to expand the
 capabilities of synthetic ultra-fast systems and provides a new framework
 to understand the behaviors of fast organisms subject to perturbations and
 environmental non-idealities.
description: This is a simulation study based on previously collected
 empirical datasets.  See the uploaded code.
description: Matlab and Mathematica
DOI: 10.5061/dryad.gqnk98ss9
title: Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron

description: Ordered transposon-insertion collections, in which specific
 transposon-insertion mutants are stored as monocultures in a genome-scale
 collection, represent a promising tool for genetic dissection of human gut
 microbiota members. However, publicly available collections are scarce and
 the construction methodology remains in the early stages of development.
 This dataset contains the raw data associated with the statistics and
 figures reported in an accompanying paper which describes the assembly of
 a genome-scale ordered collection of transposon-insertion mutants in the
 model gut anaerobe Bacteroides thetaiotaomicron VPI-5482 that we created
 as a resource for the research community.
DOI: 10.5061/dryad.08kprr560
title: Chloroplast genome assemblies and comparative analyses of commercially important Vaccinium berry crops

description: Vaccinium is a large genus of shrubs that includes a handful of
 economically important berry crops. Given the numerous hybridizations and
 polyploidization events, the taxonomy of this genus has remained the
 subject of long debate. In addition, berries and berry-based products are
 liable to adulteration, either fraudulent or unintentional due to
 misidentification of species. The availability of more genomic information
 could help achieve higher phylogenetic resolution for the genus, provide
 molecular markers for berry crop identification, and a framework for
 efficient genetic engineering of chloroplasts. Therefore, in this study,
 we assembled five Vaccinium chloroplast sequences representing the
 economically relevant berry types: northern highbush blueberry (V.
 corymbosum), southern highbush blueberry (V. corymbosum hybrids),
 rabbiteye blueberry (V. virgatum), lowbush blueberry (V. angustifolium),
 and bilberry (V. myrtillus). Comparative analyses showed that the
 Vaccinium chloroplast genomes exhibited an overall highly conserved
 synteny and sequence identity among them. Polymorphic regions included the
 expansion/contraction of inverted repeats, gene copy number variation,
 simple sequence repeats, indels, and single nucleotide polymorphisms.
 Based on their in silico discrimination power, we suggested variants that
 could be developed into molecular markers for berry crop identification.
 Phylogenetic analysis revealed multiple origins of highbush blueberry
 plastomes, likely due to the hybridization events that occurred during
 northern and southern highbush blueberry domestication.
DOI: 10.7280/d1ft44
title: Data for: Grounding zone of Amery Ice Shelf, Antarctica, from differential synthetic-aperture radar interferometry

description: We employ a time series of Sentinel-1 differential radar interferometry
 data from year 2018 to detect the variability of the grounding line
 position of the Fisher, Mellor and Lambert glaciers, which drain an ice
 volume equivalent to an 8-m sea level rise from East Antarctica. We
 observe kilometer-scale tidal migration, two orders of magnitude larger
 than expected for ice in hydrostatic equilibrium on a hard bed. The
 migration is not in phase with changes in oceanic tide. In two major
 estuaries underlaid by subglacial channels, we observe two states of
 migration that switch on and off over time scales of several weeks. The
 range of vertical motion indicates a water column thickness of 2 to 20
 centimeters. Such intrusions over wide grounding zones are not accounted
 for in physical models. Including wide grounding zone with vigorous melt
 will enhance the sensitivity of glaciers to ocean warming and increase the
 projections of mass loss.
DOI: 10.5061/dryad.zcrjdfnh6
title: Fine-scale temporal dynamics of flower visitors sheds light on the pollination strategy of a dioecious palm in the Ecuadorian Andes

description: Background: Dioecious plants generally display sexual dimorphism in male
 and female floral traits, potentially attracting slightly different
 pollinator communities. The sharing of common floral visitors between male
 and female flowers and their timing of visits to both sexes is of critical
 importance to ensure plant's reproductive success. Palm
 inflorescences are visited by abundant and diverse insect communities, yet
 the temporal patterns of insect visits on both sexes remain poorly known.
 Results: We report 59 morphospecies in the arthropod community, dominated
 by three beetle families: Staphylinidae, Nitidulidae and Curculionidae.
 Male inflorescences were more abundantly visited than female, but visitors
 of the later were taxonomically more diverse. Among the 16 pollinator
 candidates identified, 9 visited both inflorescence sexes synchronously at
 dusk /night whereas the others did so asynchronously during the day.
 Conclusion: Our study provides new insights into the pollination mechanism
 of P. aequatorialis. We found evidence of differential pollinator
 attraction between floral sexes, which may be explained by the sexual
 dimorphism of both flowers. Synchronicity in dusk/night visits of both
 inflorescence sexes suggests a sexual synchronization of the signal used
 to attract pollinators.
description: We sampled flower-visiting insects of the tagua palm Phytelephas
 aequatorialis every 4 hours from the beginning (bud opening) to the end
 (significant fading in coloration and scent of rotting tissue) of the
 anthesis of these inflorescences by using interception traps. Interception
 traps were made of a transparent foil sheet (H = 57 cm and L = 26 cm),
 stretched out between two funnels (H = 32 cm and diameter = 26 cm), and
 held vertically in the vicinity of each focal flower (Fig. 1C). The bottom
 funnel was equipped with a collector so that flying insects colliding with
 the transparent foil fell into. The collector was filled with water and a
 wetting agent acting as a surfactant to prevent captured arthropods from
 escaping. Each trap was installed from the start of the flower anthesis
 i.e., when the peduncular bract (the bud integument covering the flower)
 opened, followed by either the quick elongation for the male inflorescence
 or the revealing of the tepals for the female inflorescence (Ervik et al.
 1999). The collectors were retrieved and replaced by new ones every four
 hours. Because male flowers decay quickly, trapping was stopped within 24
 to 48 hours after the beginning of the anthesis. Female anthesis may last
 several days so that trapping was stopped 28-52h after the opening. Insect
 fauna trapped in each collector was transferred into a plastic tube and
 conserved in 70° alcohol before identification and counting in the
 lab.
DOI: 10.15468/dl.tx7mva
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Etmopterus marshae"
 ]
}

 The dataset includes 16 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003376-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6t1g1jx30
title: Population genomic analyses support sympatric origins of parapatric morphs in a salamander

description: In numerous clades, divergent sister species have largely non-overlapping
 geographic ranges. This pattern presumably arises because species diverged
 in allopatry or parapatry, prior to subsequent contact. Here we provide
 population-genomic evidence for the opposite scenario: previously
 sympatric ecotypes that have spatially separated into divergent
 monomorphic populations over large geographic scales (reverse sympatric
 scenario). We analyzed a North American salamander (Plethodon cinereus)
 with two color morphs that are broadly sympatric: striped (redback) and
 unstriped (leadback). Sympatric morphs can show considerable divergence in
 other traits, and many Plethodon species are fixed for a single morph.
 Long Island (New York) is unusual in having many pure redback and leadback
 populations that are spatially separated, with pure redback populations in
 the west and pure leadbacks in the east. Previous work showed that these
 pure-morph populations were genetically, morphologically, and ecologically
 divergent. Here, we performed a coalescent-based analysis of new data from
 88,696 single-nucleotide polymorphisms to address the origins of these
 populations. This analysis strongly supports the monophyly of Long Island
 populations and their subsequent divergence into pure redback and pure
 leadback populations. Taken together, these results suggest that the
 formerly sympatric mainland morphs separated into parapatric populations
 on Long Island, reversing the conventional speciation scenario.
description: <strong>Files for Dryad:</strong>
 <strong>File S1.</strong> Zipped directory containing
 R commands and datasets for generating figures and analyses.
 <strong>File S2.</strong> Input file with data and
 analysis settings (XML format) for SNAPP analysis of Plethodon cinereus
 from Long Island and adjacent mainland populations using all
 SNPs. <strong>File S3. </strong>Input file
 with data and analysis settings (XML format) for SNAPP analysis of
 Plethodon cinereus from Long Island and adjacent mainland populations
 using first-SNP only.   *Raw data
 from Illumunia Hi-Seq will be uploaded to the NCBI sequence read archive
 (SRA) 
description: R statistical environment BEAST 2.6.3
DOI: 10.5061/dryad.w3r2280v7
title: Data from: Human presence and infrastructure impact wildlife nocturnality differently across an assemblage of mammalian species

description: Wildlife species may shift towards more nocturnal behavior in areas of
 higher human influence, but it is unclear how consistent this shift might
 be. We investigated how humans impact large mammal diel activities in a
 heavily recreated protected area and an adjacent university-managed forest
 in southwest British Columbia, Canada. We used camera trap detections of
 humans and wildlife, along with data on land-use infrastructure (e.g.,
 recreation trails and restricted-access roads), in Bayesian regression
 models to investigate impacts of human disturbance on wildlife
 nocturnality. We found moderate evidence that black bears (Ursus
 americanus) were more nocturnal in response to human detections (mean
 posterior estimate = 0.35, 90% credible interval = 0.04 to 0.65), but no
 other clear relationships between wildlife nocturnality and human
 detections. However, we found evidence that coyotes (Canis latrans)
 (estimates = 0.81, 95% CI = 0.46 to 1.17) were more nocturnal and snowshoe
 hares (Lepus americanus) (estimate = -0.87, 95% CI = -1.29 to -0.46) were
 less nocturnal in areas of higher trail density. We also found that
 coyotes (estimate = -0.87, 95% CI = -1.29 to -0.46) and cougars (Puma
 concolor) (estimate = -1.14, 90% CI = -2.16 to -0.12) were less nocturnal
 in areas of greater road density. Furthermore, coyotes, black-tailed deer
 (Odocoileus hemionus), and snowshoe hares were moderately more nocturnal
 in areas near urban-wildland boundaries (estimates and 90% CIs: coyote =
 -0.29, -0.55 to -0.04, black-tailed deer = -0.25, -0.45 to -0.04, snowshoe
 hare = -0.24, -0.46 to -0.01). Our findings imply anthropogenic landscape
 features may influence medium to large-sized mammal diel activities more
 than direct human presence. While increased nocturnality may be a
 promising mechanism for human-wildlife coexistence, shifts in temporal
 activity can also have negative repercussions for wildlife, warranting
 further research into the causes and consequences of wildlife responses to
 increasingly human-dominated landscapes.
DOI: 10.5061/dryad.1jwstqjzp
title: Phenotypic and ecological data from: Widespread convergent morphological evolution within the largest family of songbirds

description: Although convergence is a common evolutionary phenomenon, few studies have
 quantified its prevalence across a large, densely sampled clade.
 Large-scale phylogenies and the advent of novel computational methods
 facilitate more robust identification of convergent events and their
 statistical significance. The tanagers (Aves: Thraupidae), the largest
 family of songbirds, offer an excellent opportunity to study the extent of
 phenotypic convergence in response to similar ecological pressures on a
 continental scale. To investigate convergence in the group, we used the
 largest phylogenetic and multivariate morphological dataset to date for
 the clade. First, we used phylogenetic comparative analyses to show a
 correlation between diet and aspects of bill shape. We then investigated
 our dataset for the presence and magnitude of convergent events and
 assessed significance through simulations and modeling analyses. Overall,
 we found that around half (45.3%) of species and clades we tested have
 converged in morphological space more than would be expected by chance
 alone. Our study shows that across Thraupidae, various bill shapes have
 evolved convergently to fill multiple distinct sections of ecological
 niche space, reflecting a signal of ecological opportunity and structural
 constraints.
description: The data was collected through linear measurements of museum
 specimens. It was processed in R. 
description: Rstudio (2022) R packages: PhylogeneticEM,
 mvMORPH, RColorBrewer, tidyverse, ape, geiger
DOI: 10.5061/dryad.6hdr7sr4p
title: Functional diversity of experimental annual plant assemblages drives plant responses to biological soil crusts in gypsum systems

description: 1. Biological soil crusts (BSC) are complex biotic aggregates comprised of
 lichens, cyanobacteria, algae, and other microorganism that are known to
 differently affect plant development along life cycle by selecting plant
 functional traits based on species-specific effects. In addition,
 functional differences between interacting species should modulate their
 response ability to other environmental factors. Thus, it should be
 expected that the effects of the BSC on plants will be significantly
 determined by the own functional diversity in the community. 2. To
 understand the multiple effects of BSC and the extent to which the
 functional diversity of interacting plant species can modulate their
 effects on the development of coexisting species, we applied an
 experimental approach by manipulating the initial functional diversity of
 the entire annual plant community and BSC conditions in a common garden
 trial. We crossed three sorts of assemblages built on the basis of plant
 stature (combinations of only large, or only small, or diverse sized plant
 species in pots) with three lichen-dominated BSC disturbance scenarios
 (intact, or tiny mechanically disaggregated, or absent portions of BSC).
 3. Biological soil crusts strongly affected the establishment and
 development of gypsophilous annual plants in a complex, multifaceted
 manner, which shifted throughout the plant life cycle. We demonstrated
 that lichen-dominated BSC could act as a major physical barrier to the
 establishment of annual plants at a heterogeneous fine spatial scale. Such
 a restrictive effect was particularly marked in presence of intact BSC.
 However, after annual plants overcame the restrictions imposed by BSC, the
 same biotic layer facilitated plant growth and fitness, regardless of its
 physical integrity, resulting in larger plants producing more fruits. 4.
 Importantly, our results suggest that the functional diversity structure
 of the community may also drive growth and fitness of coexisting species
 by activating alternative coexistence mechanisms such as niche
 partitioning or competition symmetry. This study highlights the importance
 of plant neighbourhood features for the performance of interacting
 species, and confirms a novel, experimental way to explore the effects of
 community diversity on plants for the interpretation of assembly
 mechanisms.
DOI: 10.5061/dryad.xpnvx0kk3
title: Data for: Genome editing of an African elite rice variety confers resistance against endemic and emerging Xanthomonas oryzae pv. oryzae strains

description: Bacterial leaf blight (BB) of rice, caused by Xanthomonas oryzae pv.
 oryzae (Xoo), threatens global food security and the livelihood of
 small-scale rice producers. Analyses of Xoo collections from Asia, Africa
 and the Americas demonstrated complete continental segregation, despite
 robust global rice trade. Here, we report unprecedented BB outbreaks in
 Tanzania. The causative strains, unlike endemic African Xoo, carry
 Asian-type TAL effectors targeting the sucrose transporter SWEET11a and
 iTALes suppressing Xa1. Phylogenomics clustered these strains with Xoo
 from Southern-China. African rice varieties do not carry effective
 resistance. To protect African rice production against this emerging
 threat, we developed a hybrid CRISPR-Cas9/Cpf1 system to edit all known
 TALe-binding elements in three SWEET promoters of the East African elite
 variety Komboka. The edited lines show broad-spectrum resistance against
 Asian and African strains of Xoo, including strains recently discovered in
 Tanzania. The strategy could help to protect global rice crops from BB
 pandemics.
description: Bacteria were sampled, and genome sequences were determined by
 whole genome sequencing. Plasmids were sequenced
 (.dna). <em>Xanthomonas</em>
 <em>oryzae</em> pv. <em>oryzae</em> strains from
 Tanzania were sequenced.  Virulence of bacteria was
 evaluated using Kauffman clipping assays and lesion length was determined
 with images and Excel files (.csv). PCR and qPCR were
 used for genotyping.
description: .dna – A DNA file is a data file created by GSL Biotech SnapGene,
 a molecular biology analysis application. It stores a DNA sequence and
 includes metadata, such as the author, a description of the sequence, and
 comments. .csv – Excel or similar.
 .fasta – text-based format for representing nucleotide
 sequences.