cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gxd2547pw
title: An unusual tandem kinase fusion protein confers leaf rust resistance in wheat

description: The introgression of chromosome segments from wild relatives is an
 established strategy to enrich crop germplasm with novel
 disease-resistance genes. Here, we use mutagenesis and transcriptome
 sequencing to clone the leaf rust resistance gene Lr9, which was
 introduced into bread wheat from the wild grass species Aegilops
 umbellulata. We establish that Lr9 encodes an unusual tandem kinase fusion
 protein. Long-read sequencing of a wheat Lr9 introgression line and the
 putative Ae. umbellulata Lr9 donor enabled us to assemble the ~28.4-Mb Lr9
 translocation and to identify the translocation breakpoint. We likewise
 cloned Lr58, which was reportedly introgressed from Ae. triuncialis, but
 has an identical coding sequence compared to Lr9. Cytogenetic and
 haplotype analyses corroborate that the two genes originate from the same
 translocation event. Our work sheds light on the emerging role of kinase
 fusion proteins in wheat disease resistance, expanding the repertoire of
 disease-resistance genes for breeding.
description: The file
 'ThatcherLr9_whole_genome_assembly.fasta.gz' contains the DNA
 sequence of the whole genome assembly of hexaploid bread wheat
 (<em>Triticum aestivum</em> L. AABBDD, 2n = 6x = 42) cv.
 Thatcher<em>Lr9</em>. The file
 'Aegilops_umbellulata_TA1851_whole_genome_assembly.fasta.gz'
 contains the DNA sequence of the whole genome assembly of diploid
 <em>Aegilops umbellulata </em>(UU, 2n = 2x = 14) accession
 TA1851. Data was produced using PacBio HiFi sequencing and assembled with
 Hifiasm. The files
 'ThatcherLr9_IsoSeq_cluster_hq.fasta.gz' and
 'TA5605_IsoSeq_cluster_hq.fasta.gz' contain high-quality
 transcript isoforms from<em> Puccinia triticina</em> infected
 leaf samples of Thatcher<em>Lr9</em> and TA5605, respectively.
 Data was produced using PacBio long-read isoform sequencing (Iso-Seq) and
 processed following the IsoSeq pipeline (v.3.; https://github.com/PacificBiosciences/IsoSeq). The<em> Lr9</em> CDS and genomic sequences are present in FASTA format.
DOI: 10.5061/dryad.44j0zpch4
title: Allometric scaling of a superposition eye optimises sensitivity and acuity in large and small hawkmoths

description: Animals vary widely in body size within and across species. This has
 consequences for the function of organs and body parts in both large and
 small individuals. How these scale, in relation to body size, reveals
 evolutionary investment strategies, often resulting in trade-offs between
 functions. Eyes exemplify these trade-offs, as they are limited by their
 absolute size in two key performance features: sensitivity and spatial
 acuity. Due to their size polymorphism, insect compound eyes are ideal
 models for studying the allometric scaling of eye performance. Previous
 work on apposition compound eyes revealed that allometric scaling led to
 poorer spatial resolution and visual sensitivity in small individuals,
 across a range of insect species. Here, we used X-ray microtomography to
 investigate allometric scaling in superposition compound eyes – the second
 most common eye type in insects – for the first time. Our results reveal a
 novel strategy to cope with the trade-off between sensitivity and spatial
 acuity, as we show that the eyes of the hummingbird hawkmoth retain an
 optimal balance between these performance measures across all body sizes.
description: see Methods in the linked publication
DOI: 10.5061/dryad.c2fqz61bx
title: Methodological confounds of measuring urinary oxidative stress in wild animals

description: Biomarkers of oxidative stress (OS) are useful in addressing a wide range
 of research questions, but thus far, they have had limited application to
 wild mammal populations due to a reliance on blood or tissue sampling. A
 shift towards non-invasive measurement of OS would allow field ecologists
 and conservationists to apply this method more readily. However, the
 impact of methodological confounds on urinary OS measurement under field
 conditions has never been explicitly investigated. We combined a
 cross-sectional analysis with a field experiment to assess the impact of
 four potential methodological confounds on OS measurements: 1) time of
 sampling, 2) environmental contamination from foliage; 3) delay between
 sample collection and flash-freezing in liquid nitrogen; 4) sample storage
 of up to 15 months below -80C. We measured DNA oxidative damage
 (8-hydroxy-2’-deoxyguanosine, 8-OHdG), lipid peroxidation
 (malondialdehyde, MDA), Total Antioxidant Capacity (TAC) and uric acid
 (UA) in 167 urine samples collected from wild Zanzibar red colobus
 (Piliocolobus kirkii). We found that MDA was higher in samples collected
 in the morning than in the afternoon but there were no diurnal patterns in
 any of the other markers. Contamination of samples from leaf surfaces and
 time frozen at -80°C for up to 15 months did not affect OS marker
 concentrations. Freezing delay did not affect OS levels cross-sectionally,
 but OS values from individual samples showed only moderate to good
 consistency and substantial rank order reversals when exposed to different
 freezing delays. We recommend that the impact of storage time on OS marker
 concentrations and diurnal patterns of OS markers be considered when
 designing sampling protocols. However, given the high stability we
 observed for four OS markers subject to a variety of putative
 methodological confounds, we suggest that urinary OS markers provide a
 valuable addition to the toolkit of field ecologists and conservationists
 within reasonable methodological constraints.
description: Data files have been uploaded as .csv files and so can be opened
 in any spreadsheet program.
DOI: 10.5061/dryad.9w0vt4bjb
title: Two simple movement mechanisms for spatial division of labour in social insects

description: Many animal species divide space into a patchwork of home ranges, yet
 there is little consensus on the mechanisms individuals use to maintain
 fidelity to particular locations. Theory suggests that animal movement
 could be based upon simple behavioural rules that use local information
 such as olfactory deposits, or global strategies, such as long-range
 biases toward landmarks. However, empirical studies have rarely attempted
 to distinguish between these mechanisms. Here, we perform individual
 tracking experiments on four species of social insects, and find that
 colonies consist of different groups of workers that inhabit separate but
 partially-overlapping spatial zones. Our trajectory analysis and
 simulations suggest that worker movement is consistent with two local
 mechanisms: one in which workers increase movement diffusivity outside
 their primary zone, and another in which workers modulate turning
 behaviour when approaching zone boundaries. Parallels with other organisms
 suggest that local mechanisms might represent a universal method for
 spatial partitioning in animal populations.
description: Individual trajectories collected by automated tracking using
 barcode tags.  See the Methods section in the main
 paper, the Supporting Information and the Nature Reporting Summary for
 details on the tracking.
description: This repository contains the raw data for the
 publication: Richardson, T.O., Stroeymeyt, N.S.,
 Crespi, A., & Keller, L. "Two simple movement mechanisms for
 spatial division of labour in social insects". Nature Communications.
 In press. Code for constructing the bipartite spatial
 networks, and for the simulations can be found in the following Zenodo
 repository: https://doi.org/10.5281/zenodo.6787674
DOI: 10.5061/dryad.r2280gbg4
title: Ellipsoid body subset neurons induce pivot behaviour in Drosophila

description: Many animals maintain certain forms of internal compass. The ellipsoid
 body in the central complex of the fruit fly, Drosophila melanogaster, is
 considered to receive and process multiple signals for orientation and
 navigation. Here we report the pivot behaviour, where a free moving fly
 keeps turning near a fixed point upon activation of neurons in the central
 complex. Using clonal analysis, we narrowed down the responsible neurons
 to a specific class of ellipsoid body neurons, ER2_c. A trans-synaptic
 tracing analysis indicated that these neurons are connected downstream to
 structures estimating head direction in the recent ring attractor model.
 Together, we identified ER2_c responsible for pivot behaviour, furtherly,
 our results provided evidence that ring neurons manage inherent
 directions, which contributed to a deeper picture of ring attractor model.
description: There are two parts in this dataset, first is the MATLAB scripts
 to extract movement information of flies, and the second part is the
 suorce data to analyse the significancy between pivot flies and control
 flies.
DOI: 10.5061/dryad.7m0cfxpxb
title: Dataset on foraging ecology of shrubland bird community

description: Habitat loss due to increasing anthropogenic disturbance is the major
 driver for bird population declines across the globe. Within the Eastern
 Ghats of India, shrubland bird communities are threatened by shrinking of
 suitable habitats due to increased anthropogenic disturbance and climate
 change. Development of an effective habitat management strategy is
 hampered by the absence of data for this bird community. To address this
 knowledge gap, we examined foraging sites for 14 shrubland bird species,
 including three declining species, in three study areas representing the
 shrubland type of forest community in the Eastern Ghats. We recorded
 microhabitat features within an 11 m radius of observed foraging points
 and compared these data with similar data from random plots. We used
 chi-square to test the association between plant species and bird species
 for sites where they were observed foraging. We observed significant
 differences between foraging sites of all the study species and random
 plots, thus indicating selection for foraging habitat. Using linear
 discriminant analysis, we found that the microhabitat features important
 for the bird species were shrub density, vegetational height, vertical
 foliage stratification, grass height, and percent rock cover. Our results
 show that diet guild and foraging strata influence the foraging
 microhabitat selection of a species (e.g., ground-foraging species
 differed significantly from other species). Except for two species, all
 focal birds were associated with at least one plant species. The
 plant-bird association was based on foraging, structural, or behavioral
 preferences. Several key factors affecting foraging habitat such as shrub
 density can be actively managed at the local scale. Strategic and
 selective harvesting of forest products and a spatially and temporally
 controlled livestock grazing regime may allow regeneration of scrubland
 and create conditions favorable to birds.
DOI: 10.5061/dryad.qnk98sfkf
title: Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya

description: Background Livestock systems have been proposed as a reservoir for
 antimicrobial-resistant (AMR) bacteria and AMR genetic determinants that
 may infect or colonise humans, yet quantitative evidence regarding their
 epidemiological role remains lacking. Here we used a combination of
 genomics, epidemiology and ecology to investigate patterns of AMR gene
 carriage in Escherichia coli, regarded as a sentinel organism. Methods We
 conducted a structured epidemiological survey of 99 households across
 Nairobi, Kenya, and whole genome sequenced E. coli isolates from 311
 human, 606 livestock, and 399 wildlife faecal samples. We used statistical
 models to investigate the prevalence of AMR carriage and characterise AMR
 gene diversity and structure of AMR genes in different host populations
 across the city. We also investigated house-hold level risk factors for
 exchange of AMR genes between sympatric humans and livestock. Findings We
 detected 56 unique acquired genes along with 13 point mutations present in
 variable proportions in human and animal isolates, known to confer
 resistance to nine antibiotic classes. We find that AMR gene community
 composition is not associated with host species, but AMR genes were
 frequently co-located, potentially enabling the acquisition and dispersal
 of multi-drug resistance in a single step. We find that whilst keeping
 livestock had no influence on human AMR gene carriage, the potential for
 AMR transmission across human-livestock interfaces is greatest when manure
 is poorly disposed of and in larger households. Conclusions Findings of
 widespread carriage of AMR bacteria in human and animal populations,
 including in long-distance wildlife species, in community settings,
 highlight the value of evidence-based surveillance to address
 antimicrobial resistance on a global scale. Our genomic analysis provided
 in-depth understanding of AMR determinants at the interfaces of One-Health
 sectors that will inform AMR prevention and control.
description: Data contains sample ID, source types (Source_Level1 contains the granular
 species group, Source_Level2 contains grouping of the species data further
 into humans, monogastrics which include pigs and rabbits, ruminants which
 include cattle, sheep, and goats, w_avian which includes wildlife avian
 i.e. birds, w_bats which include wildlife bats i.e. bats; Source_Level3
 contains three groups, humans, livestock, and wildlife; Source_Level4
 contains functional groups humans, livestock birds, livestock mammals,
 wild bird), livestock type present in the household, and predicted
 antibiotic resistance genes.
DOI: 10.5061/dryad.d7wm37q44
title: Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)

description: Subfamily Rubioideae is the largest of the main lineages in the coffee
 family (Rubiaceae), with over 8,000 species and 29 tribes. Phylogenetic
 relationships among tribes and other major clades within this group of
 plants are still only partly resolved despite considerable efforts. While
 previous studies have mainly utilized data from the organellar genomes and
 nuclear ribosomal DNA, we here use a large number of low-copy nuclear
 genes obtained via a target capture approach to infer phylogenetic
 relationships within Rubioideae. We included 101 Rubioideae species
 representing all but two (the monogeneric tribes Foonchewieae and
 Aitchinsonieae) of the currently recognized tribes, and all but one
 non-monogeneric tribe were represented by more than one genus. Using data
 from the 353 genes targeted with the universal Angiosperms353 probe set we
 investigated the impact of data type, analytical approach, and potential
 paralogs on phylogenetic reconstruction. We inferred a robust phylogenetic
 hypothesis of Rubioideae with the vast majority (or all) nodes being
 highly supported across all analyses and datasets and few incongruences
 between the inferred topologies. The results were similar to those of
 previous studies but novel relationships were also identified. We found
 that supercontigs (coding sequence [CDS] + noncoding sequence) clearly
 outperformed CDS data in levels of support and gene tree congruence. The
 full datasets (353 genes) outperformed the datasets with potential
 paralogous genes removed (186 genes) in levels of support but increased
 gene tree incongruence slightly. The pattern of gene tree conflict at
 short internal branches was often consistent with high levels of
 incomplete lineage sorting (ILS) due to rapid speciation in the group.
 While concatenation- and coalescence-based trees mainly agreed, the
 observed phylogenetic discordance between the two approaches may be best
 explained by their differences in accounting for ILS. The use of target
 capture data greatly improved our confidence and understanding of the
 Rubioideae phylogeny, highlighted by the increased support for previously
 uncertain relationships and the increased possibility to explore sources
 of underlying phylogenetic discordance.
description: The data was collected using a target capture approach (using the
 Angiosperms 353 probe set). The sequences were assembled using HybPiper
 (Johnson et al. 2016).
description: This dataset includes assembled sequences (CDS and supercontigs)
 and the target file used for HybPiper assembly.
DOI: 10.5061/dryad.n02v6wx0v
title: Data for: Intergenerational genotypic interactions drive collective behavioural cycles in a social insect

description: Many social animals display collective activity cycles based on
 synchronous behavioural oscillations across group members. A classic
 example is the colony cycle of army ants, where thousands of individuals
 undergo stereotypical biphasic behavioural cycles of about one month.
 Cycle phases coincide with brood developmental stages, but the regulation
 of this cycle is otherwise poorly understood. Here, we probe the
 regulation of cycle duration through interactions between brood and
 workers in an experimentally amenable army ant relative, the clonal raider
 ant. We first establish that cycle length varies across clonal lineages
 using long-term monitoring data. We then investigate the putative sources
 and impacts of this variation in a cross-fostering experiment with four
 lineages combining developmental, morphological, and automated behavioural
 tracking analyses. We show that cycle length variation stems from
 variation in the duration of the larval developmental stage, and that this
 stage can be prolonged not only by the clonal lineage of brood (direct
 genetic effects), but also of the workers (indirect genetic effects). We
 find similar indirect effects of worker line on brood adult size and,
 conversely but more surprisingly, indirect genetic effects of the brood on
 worker behaviour (walking speed and time spent in the nest).
description: Files can be accessed using R and MATLAB.
DOI: 10.5061/dryad.zs7h44jcp
title: Comparative efficacy of GS-Hv1a against invasive tropical tephritids

description: Invasive tephritid fruit flies collectively pose a significant economic
 challenge to agricultural pest management globally. Insecticide resistance
 to a number of previously effective chemical classes has increased the
 risk these pests pose as management options become limited. We evaluated
 the efficacy of a novel class of peptide-based biorational insecticides
 containing the active ingredient, GS-omega/kappa-Hxtx-Hv1a (Hv1a), against
 four of tephritid species, oriental fruit fly (Bactrocera dorsalis), melon
 fly (Zeugodacus cucurbitae), Mediterranean fruit fly (Ceratitis capitata,
 “Medfly”), and Malaysian fruit fly (B. latrifrons). This assessment aimed
 to determine whether Hv1a has the potential for effective management of
 tropical tephritids, particularly in regions where insecticide resistance
 has developed to other products. We conducted two sets of screening assays
 with different methods of exposure, oral and topical, and compared
 survival over time in response to increasing concentrations of Hv1a up to
 3.86 mg/ml. We found that efficacy was species dependent: Ceratitis
 capitata was susceptible following topical exposure, while the other
 species of fruit fly were not. While Medfly was susceptible following oral
 ingestions as well, the dose required to achieve mortality was greater
 than topical. We observed that mortality continued to decline up to 72
 hours after exposure, indicating a delayed effect similar to other
 reduced-risk insecticidal products such as fipronil. For this reason, Hv1a
 may be useful as a horizontal transfer tool in conjunction with C.
 capitata male pheromone lures.
description: All data analysis was performed using R version 4.1.3 “One
 Push-Up”, R Core Team (2021). R: A language and environment for
 statistical computing. R Foundation for Statistical Computing, Vienna,
 Austria; https://www.R-project.org/). Probit analysis using the package “ecotox” (Hlina et al., 2021) was used to calculate LC50 values for each tephritid species. Survival analysis was conducted using Cox proportional hazards models with the packages “survival” (Therneau, 2022; Therneau & Grambsch, 2000) and “survminer” (Kassambara et al., 2021). Posthoc analysis was conducted using the package “emmeans” (Lenth, 2022) to determine pairwise differences in significance between concentrations for each species.
DOI: 10.5061/dryad.fxpnvx0vs
title: Temperate zone isolation by climate: an extension of Janzen’s 1967 hypothesis

description: One of the most stunning patterns of the distribution of life on Earth is
 the latitudinal biodiversity gradient. In an influential paper, Janzen
 (1967) predicted that tropical mountains are more effective migration
 barriers than temperate mountains of the same elevation because annual
 temperature variation in the tropics is lower. A great deal of research
 has demonstrated that the mechanism envisioned by Janzen operates at broad
 latitudinal scales. However, the extent that the mechanism mediates
 biodiversity generally, and at smaller scales, is far less understood. We
 investigated if climate overlap is associated with genetic similarity
 between populations within temperate regions using lizards in the Sierra
 Nevada mountain range, California, as a study system. By comparing genetic
 differentiation between high- and low-elevation populations, we found that
 in addition to the expected strong pattern of isolation by distance (IBD),
 climate overlap values were negatively associated with genetic
 differentiation, indicating that population pairs that inhabit
 climatically similar environments are less genetically differentiated.
 Moreover, while climate overlap between high- and low-elevation sites is
 predicted to increase from the equator to temperate regions, we find that
 in adjacent mountain ranges at the same latitude in temperate regions,
 climate overlap values can vary widely. This study suggests that in
 addition to the well-studied main effect of latitude on climate overlap
 and population differentiation, local climate factors within bioclimatic
 regions can also influence genetic differentiation between populations,
 and do so by the same general mechanism that operates at larger geographic
 scales.
description: This dataset was collected by double-digest restriction-site
 associated DNA sequencing (ddRAD-seq) of western fence lizards (Sceloporus
 occidentalis) in California, USA.
description: No proprietary software is needed to open the data files
 included.