cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3r2280gnh
title: Variation among strains of Borrelia burgdorferi in host tissue abundance and lifetime transmission determine the population strain structure in nature

description: Pathogen life history theory assumes a positive relationship between
 pathogen load in host tissues and pathogen transmission. Empirical
 evidence for this relationship is surprisingly rare due to the difficulty
 of measuring transmission for many pathogens. The comparative method,
 where a common host is experimentally infected with a set of pathogen
 strains, is a powerful approach for investigating the relationships
 between pathogen load and transmission. The validity of such experimental
 estimates of strain-specific transmission is greatly enhanced if they can
 predict the pathogen population strain structure in nature. Borrelia
 burgdorferi is a multi-strain, tick-borne spirochete that causes Lyme
 disease in North America. This study used 11 field-collected strains of B.
 burgdorferi, a rodent host (Mus musculus, C3H/HeJ) and its tick vector
 (Ixodes scapularis) to determine the relationship between pathogen load in
 host tissues and lifetime host-to-tick transmission (HTT). Mice were
 experimentally infected via tick bite with 1 of 11 strains. Lifetime HTT
 was measured by infesting mice with I. scapularis larval ticks on 3
 separate occasions. The prevalence and abundance of the strains in the
 mouse tissues and the ticks were determined by qPCR. We used published
 databases to obtain estimates of the frequencies of these strains in wild
 I. scapularis populations. Spirochete loads in ticks and lifetime HTT
 varied significantly among the 11 strains of B. burgdorferi. Strains with
 higher spirochete loads in the host tissues were more likely to infect
 feeding larvae, which molted into nymphs with a higher probability of B.
 burgdorferi infection (i.e., higher HTT). Our laboratory-based estimates
 of lifetime HTT were predictive of the frequencies of these strains in
 wild I. scapularis populations. For B. burgdorferi, the strains that
 establish high abundance in host tissues and that have high lifetime
 transmission are the strains that are most common in nature.
description: See the 'Read me' markdown file and the manuscript for
 explanations of how these datasets were collected and processed.
description: The raw data are stored in 5 different Microsoft Excel files. See
 the 'Read me' markdown file for an explanations of the variables
 in the Excel files.
DOI: 10.5061/dryad.cnp5hqc9p
title: Genetic architecture and polygenic risk score prediction of degenerative suspensory ligament desmitis (DSLD) in the Peruvian Horse

description: Introduction: Spontaneous rupture of tendons and ligaments is common in
 several species including humans. In horses, degenerative suspensory
 ligament desmitis (DSLD) is an important acquired idiopathic disease of a
 major energy-storing tendon-like structure. DSLD risk is increased in
 several breeds, including the Peruvian Horse. Affected horses have often
 been used for breeding before the disease is apparent. Breed
 predisposition suggests a substantial genetic contribution, but
 heritability and genetic architecture of DSLD have not been determined.
 Methods: To identify genomic regions associated with DSLD, we recruited a
 reference population of 183 Peruvian Horses, phenotyped as DSLD cases or
 controls, and undertook a genome-wide association study (GWAS), a regional
 window variance analysis using local genomic partitioning, a signatures of
 selection (SOS) analysis, and polygenic risk score (PRS) prediction of
 DSLD risk. We also estimated trait heritability from pedigrees. Results:
 Heritability was estimated in a population of 1,927 Peruvian horses at
 0.22±0.08. After establishing a permutation-based threshold for
 genome-wide significance, 151 DSLD risk single nucleotide polymorphisms
 (SNPs) were identified by GWAS. Multiple regions of enriched local
 heritability were identified across the genome, with strong enrichment
 signals on chromosomes 1, 2, 6, 10, 13, 16, 18, 22, and the X chromosome.
 With SOS analysis, there were 66 genes with a selection signature in DSLD
 cases that was not present in the control group that included the TGFB3
 gene. Pathways enriched in DSLD cases included proteoglycan metabolism,
 extracellular matrix homeostasis, and signal transduction pathways that
 included the hedgehog signaling pathway. The best PRS predictive
 performance was obtained when we fitted 1% of top SNPs using a Bayesian
 Ridge Regression model which achieved the highest mean of R2 on both the
 probit and logit liability scales, indicating a strong predictive
 performance. Discussion: We conclude that within-breed GWAS of DSLD in the
 Peruvian Horse has further confirmed that moderate heritability and a
 polygenic architecture underlies the trait and identified multiple DSLD
 SNP associations in novel tendinopathy candidate genes influencing disease
 risk. Pathways enriched with DSLD risk variants include ones that
 influence glycosaminoglycan metabolism, extracellular matrix homeostasis,
 and signal transduction pathways.
description: Peruvian Horses were recruited with IACUC approval and phenotyped
 as degenerative suspensory ligament desmitis cases or phenotype-negative
 controls. Genome-wide SNP genotypes were generated from DNA samples that
 were assayed using an equine genotyping array.
description: Plink binary file sets can be analyzed with PLINK or other
 similar analytical software.
DOI: 10.5061/dryad.rbnzs7hhk
title: CanineHD 230 K BeadChip data from Pembroke Welsh corgi

description: Several hundred disease-causing mutations are currently known in domestic
 dogs. Breeding management is therefore required to minimize their spread.
 Recently, genetic methods such as direct-to-consumer testing have gained
 popularity; however, their effects on dog populations are
 unclear.  Here, we aimed to evaluate the influence of genetic
 testing on the frequency of mutations responsible for canine degenerative
 myelopathy (DM) and assess the changes in the genetic structure of a
 Pembroke Welsh corgi population from Japan. To evaluate the influence of
 genetic testing on the frequency of mutations causing canine degenerative
 myelopathy and changes to genetic structure in the Pembroke Welsh corgi
 population from Japan, 117 dogs were genotyped. Weir and Cockerham
 population differentiation (FST) based on genome-wide single-nucleotide
 polymorphism (SNP) detected the SNP with the highest FST located in the
 intron of SOD1 adjacent to the c.118G&gt;A mutation, supporting a
 selection signature on SOD1. Further genome-wide SNP analyses revealed no
 obvious changes in inbreeding levels between the 2019 and 2022
 populations. Our study highlights that genetic testing can help inform
 improved mating choices in breeding programs to reduce the frequency of
 risk variants and avoid inbreeding.
description: 142,510 single nucleotide
 polymorphism (SNP) of 112 dogs by using Illumina's Canine 230K
 Consortium chip.
description: Illumina's Canine 230K Consortium BeadChip data from 117 dogs. The
 breed is Pembroke Welsh corgi from Japan. corgi_DM_QC.ped : PLINK ped file
 corgi_DM_QC.map : PLINK map file
DOI: 10.5061/dryad.qnk98sfns
title: Late instar monarch caterpillars sabotage milkweed to acquire toxins, not to disarm plant defence

description: Sabotaging milkweed by monarch caterpillars (Danaus plexippus) is a famous
 textbook example of disarming plant defence. By severing leaf veins,
 monarchs are thought to prevent the flow of toxic latex to their feeding
 site. Here, we show that sabotaging by monarch caterpillars is not only an
 avoidance strategy. While young caterpillars appear to avoid latex,
 late-instar caterpillars actively ingest exuding latex, presumably to
 increase sequestration of cardenolides used for defence against predators.
 Comparisons with caterpillars of the related but non-sequestering
 common crow butterfly (Euploea core) revealed three lines of evidence
 supporting our hypothesis. First, monarch caterpillars sabotage
 inconsistently and therefore the behaviour is not obligatory to feed on
 milkweed, whereas sabotaging precedes each feeding event in Euploea
 caterpillars. Second, monarch caterpillars shift their behaviour from
 latex avoidance in younger to eager drinking in later stages, whereas
 Euploea caterpillars consistently avoid latex and spit it out during
 sabotaging. Third, monarchs reared on detached leaves without latex,
 sequestered more cardenolides when caterpillars imbibed latex offered with
 a pipette. Thus, we conclude that monarch caterpillars have transformed
 the ancestral ‘sabotage to avoid’ strategy into a ‘sabotage to consume’
 strategy implying a novel behavioural adaptation to increase sequestration
 of cardenolides for defence.
description: Readme for the statistical documentation for the publication: Monarchs
 sabotage milkweed to acquire toxins, not to disarm plant defense Authors:
 Anja Betz, Robert Bischoff, Georg Petschenka For the statistical
 documentation, we provide the following files: This readme gives a brief
 outline of the different files and data provided in the statistical
 documentation Subfolders for each experiment containing * Excel files with
 just the data, SAS code files for analysis of each dataset with comments
 SAS dataset files (sas7bdat) a data dictionary.txt that defines all
 variables of all datasets Disclaimer: Excel automatically formats numbers.
 We do not take any responsibility for automatic formatting of the numbers
 by Excel. This might lead to different results, if the Excel files are
 used for analysis. The sas7bdat files, or data at the start of the
 individual sas-analysis files should be resistant to automatic formatting,
 so we suggest using them for analysis. The datasets collected in the
 corresponding experiments share the same latter as the experiment: i.
 Sabotaging behavior over the ontogeny ii. Artificial latex feeding and
 petiole cutting duration iii. Efficiency of latex-removal iv. Latex
 drinking during vein-cutting v. Latex drinking and butterfly toxicity vi.
 Latex influence on larval instars vii. Petiole cutting duration of last
 instars Appendix data: Determination of latex outflow
DOI: 10.5061/dryad.pvmcvdnrf
title: Mitochondrial ND2 sequences from 40 specimens of six Onychorhynchus coronatus lineages: swainsoni, coronatus, castelnaui, mexicanus, occidentalis, and fraterculus

description: We examined phylogeographic patterns and cryptic diversity within the
 royal flycatcher, Onychorhynchus coronatus (Aves: Onychorhynchidae), a
 widespread Neotropical lowland forest tyrant flycatcher. A phylogeny of
 the six recognized subspecies was constructed from mtDNA sequence data of
 the NADH dehydrogenase subunit two gene, using Bayesian Inference and
 Maximum Likelihood methods. Phylogenetic analyses revealed high levels of
 intraspecific divergence within O. coronatus, supporting the existence of
 at least six independent lineages. The phylogenetic results uncovered the
 following relationships: (O. c. swainsoni [Southern Atlantic Forest], (O.
 c. coronatus [western Amazonia], (O. c. castelnaui [eastern Amazonia], (O.
 c. mexicanus [Central America], (O. c. occidentalis [Tumbesian], O. c.
 fraterculus [extreme northwestern South America])))). Biogeographic and
 dating analyses suggest that vicariant and dispersal events acted across
 approximately six million years to influence lineage diversification
 within this genus. Some of those events include the formation of the
 Amazon River and its tributaries, Andean uplift, and climatically induced
 vegetational shifts. Phylogenetic and biogeographic analyses of O.
 coronatus lineages support a hypothesis of area relationships in which the
 first divergence event isolated the Southern Atlantic Forest from Amazonia
 during the Late Miocene/Early Pliocene. This event was followed by the
 split of western and eastern Amazonia at the Early/Late Pliocene, the
 divergence of cis- and trans-Andean lowland regions also at the Early/Late
 Pliocene, the split between Central America and the extreme northwestern
 South America/Tumbes at the Early/Middle Pleistocene, and the split
 between extreme northwestern South America and Tumbes at Middle/Late
 Pleistocene. Subsequent divergence of the southern and northern
 populations in the western and eastern Onychorhynchus lineages took place
 during the Pleistocene. Comparison of phylogenetic trees and patterns in
 Onychorhynchus with those from published work suggests that across large
 New World radiations such as the Suboscines, some co-distributed lineages
 began to diverge long before others, which exemplifies the complexity of
 their evolutionary history.
description: Sanger sequencing. Sequences were reviewed and aligned using the
 program Geneious (Biomatters, Inc.).
description: Any program that opens Nexus files.
DOI: 10.5061/dryad.h18931zs4
title: Afromontane understory birds increase in body size over four decades

description: Of the myriad responses to climate change, an emerging trend is the
 widespread decrease in animal body size with warming temperatures. Birds,
 in particular, have been shown to be decreasing in body size in several
 areas – most notably the Amazon Basin and temperate North America – but
 trends in much of the world remain unexplored. Here, we analyze temporal
 trends in and climatic associations of body mass for 42 resident bird
 species over 36 years in the Usambara Mountains of Tanzania, a tropical
 montane global biodiversity hotspot. In addition, we assess trends in wing
 length and mass:wing ratio over 21 years. Finally, we examine whether
 species-specific trends in body mass are related to average body size or
 to trends in apparent survival. Overall, species’ average body mass in the
 Usambara Mountains increased by 0.023 g/decade, amounting to increases of
 4.1% over 36 years. These long-term shifts in body mass were strongly and
 positively associated with annual mean temperature but showed no
 relationship with precipitation. Wing length increased on average by 2.0%
 over the most recent 21-year period, yet there was mixed evidence for
 trends in mass:wing ratio, suggesting that body size, in general, is
 increasing. While percentage trends in body mass were not related to
 trends in apparent annual survival, smaller species did display greater
 proportional increases in body mass. Although the drivers of increased
 body size remain unclear – and climate change cannot be ruled out – such
 increases among Afrotropical montane birds provide an intriguing
 counterpoint to observed declines in body mass elsewhere and suggest that
 trends in body mass in tropical birds may be mediated by biogeography or
 other abiotic or biotic drivers.
description: # Body mass of Tanzanian birds --- This dataset comprises the body mass
 and wing length measurements of 42 Afromontane bird species taken over 36
 years in the Usambara Mountains of Tanzania. ## Description of the Data
 and file structure The dataset comprises eight columns. * A: an
 "order" column to return data to the original ordering. * B: the
 initials of the bander who weighed the bird. * C: binary location, either
 EU (East Usambaras) or WU (West Usambaras). * D: the year, starting at
 0=1987. * E: the site; redundant as 16=EU and 23=WU. * F: species, based
 Clements taxonomy. * G: bird weight (g). * H: wing length (cm).
DOI: 10.5061/dryad.k6djh9wcd
title: Source height and contact with terrestrial soil drive transplanted epiphyte performance

description: Epiphytes are characterized by their ability to survive without a root
 connection to the ground, but many basic life-history traits and
 ecological trade-offs of this unique aerial growth habit remain largely
 uncharacterized. Mortality causes are still not well understood, but
 falling from the host tree has been suggested as a leading cause of
 epiphyte mortality and community dynamics. Little empirical evidence
 exists for why epiphytes do not survive when forced to become
 terrestrial, and few studies exist that transplant epiphytes between high-
 and low-forest strata to test trade-offs between thriving in canopy
 environments and survival in the forest understory. Here, we
 experimentally test two hypotheses regarding the drivers of epiphyte
 mortality in a cloud forest of central Panama. We test whether simple
 contact with terrestrial soil is deleterious to epiphytes, preliminarily
 testing the Epiphyte Enemy Escape Hypothesis, and test the Vertical Niche
 Differentiation Hypothesis, wherein epiphytes are specifically adapted for
 microsites throughout the vertical forest strata. By monitoring survival,
 leaf loss, and health status of 270 transplanted epiphytes for a year and
 a half, we pinpoint the extent to which soil contact and height of origin
 regulate epiphyte performance.  We found that contact with
 terrestrial soil itself was detrimental to epiphytes in situ, providing
 some of the first empirical data to explain why falling onto the ground,
 versus falling into the understory, is particularly fatal to epiphytes.
 However, we also found that mortality rates vary substantially among
 taxonomic groups and among epiphytes that originally came from different
 height strata. Synthesis. Plants that are adapted for the canopy
 experience a trade-off with higher mortality when in contact with
 terrestrial soil. Follow-up studies should explore the role of terrestrial
 soil microbes and physiological constraints as potential drivers of
 decreased grounded epiphyte survival. 
description: Data were collected in 2017-2018 by MES & JAO in the
 Santa Fe National Park, Veraguas, Panama. Survival, number of leaves, and
 health status (on a scale of 0–2), of 270 epiphytes transplanted at 0, 1,
 or 2m were tracked for 77 weeks, ~weekly or biweekly and then less
 frequently later on. This dataset consists of the wide-form data
 summarized to individual epiphytes at the end of the 77-week
 experiment.
description: R, R Studio
DOI: 10.5061/dryad.vdncjsz14
title: White shark diet sequences and sequence library

description: The white shark (Carcharodon carcharias) is one of the world's
 largest apex predators found throughout the world's temperate and
 subtropical marine environments. However, the species has suffered
 significant declines in recent decades and effective conservation programs
 require a sound knowledge of white shark biology and ecology. In
 particular, information on white shark diet across life stages and the
 species' range is needed to identify critical trophic interactions
 supporting shark populations and to predict the resilience of white sharks
 to environmental changes. In this study, we reassess the diet and trophic
 ecology of white sharks via the genetic analyses of cloacal swabs from 214
 juvenile and subadult sharks from eastern Australia. Our findings are
 largely consistent with those of previous studies based on visual analyses
 of gut contents but highlight the unprecedented taxonomic resolution of
 prey items offered by genomic assessments of shark cloacal swabs. Diets
 consisted primarily of ray-finned fishes, with Mugiliformes,
 Carangiformes, Perciformes, and Scombriformes being dominant prey taxa,
 but with elasmobranchs, marine mammals, and birds also being common
 dietary constituents. Statistical analyses revealed a significant effect
 of sex and sampling location on diet composition, indicating biological
 and spatial variability in diets and predatory behavior. Overall, these
 findings support the notion that juvenile and subadult white sharks are
 opportunistic predators, which may provide some level of resilience to
 shifts in marine resources. However, frequently consumed ray-finned
 fishes, many of which are commercially targeted, may be key to supporting
 white shark populations in eastern Australia. This study represents the
 most comprehensive analysis of juvenile and subadult white shark diets
 performed to date and provides added confidence in the genomic analysis of
 cloacal swabs for dietary assessments of predatory species. These results
 are expected to help inform management geared toward conserving this
 important marine predator across the world's oceans.
DOI: 10.5061/dryad.9cnp5hqq7
title: Cultural atlas of vocal variation in the yellow-naped amazon parrot

description: Vocal dialects are a taxonomically widespread phenomenon, which are
 usually studied in a restricted portion of a species’ range. It is unclear
 whether geographic patterns observed in one part of a species’ range can
 be inferred as typical across the range or whether local conditions
 influence the presence or absence of dialects. We examined the
 yellow-naped amazon, Amazona auropalliata, a parrot species with
 remarkable vocal learning capabilities. Although this species is native to
 Mesoamerica, only Costa Rican populations have been evaluated long-term.
 Previous studies have shown that these populations exhibit geographically
 and temporally stable vocal dialect patterns. Without data on populations
 outside of Costa Rica, it is impossible to know if vocal dialects are
 present in northern range populations, and whether or not they exhibit
 similar geographic structure to southern range populations. We recorded
 yellow-naped amazon contact calls at 47 different sites across the range
 between 2016 and 2019 and evaluated them for the presence of dialects. We
 visually classified 14 contact call types based on spectrographic
 similarity and used spectrographic cross-correlation, principal component
 analysis, and Mantel-based spatial autocorrelations to assess acoustic
 similarity. The results from our study show that the vocal patterns
 previously seen in Costa Rica are also present in northern range
 populations, supporting our hypothesis. Call types were regionally
 specific (e.g., vocal dialects) across the range, and no call types were
 repeated across multiple regions. We did, however, observe distinctive
 structural characteristics that are found in multiple call types,
 suggesting that different call types stem from a common origin. Vocal
 dialect in this species is likely maintained through a tendency toward
 philopatry and matching call types to enhance social identification.
DOI: 10.5061/dryad.ksn02v79j
title: Data from: The role of male body size in mating success and male-male competition in a false widow spider

description: In many animals, body size is correlated with reproductive success.
 Selection sometimes generates striking differences in body size between
 males and females (i.e., sexual size dimorphism, SSD). SSD is common in
 spiders (Araneae), and is typically explained by selection for larger,
 more fecund females, and rapidly maturing, and consequently smaller males.
 Within a species males and females also often vary in body size. 
 In the false widow spider (Steatoda grossa), females are larger than males
 and males trade off body size for rapid development and early maturation.
 Moreover, males exhibit considerable variation in body size, suggesting
 that under certain conditions there may be advantages to large size. Here,
 we tested the role of male body size on mating success under
 non-competitive and competitive mating conditions (i.e., male-male
 competition) in S. grossa. We found that body size did not influence
 mating success or copulation duration under non-competitive conditions,
 but that larger males were more successful at obtaining access to females
 under competitive mating conditions. Additionally, we found that total
 copulation duration was significantly lower when a rival male was present.
 Our results show a large male advantage under male-male competition, which
 we suggest may contribute to the high variation in male body size observed
 in S. grossa. We further suggest that the reduced copulation duration
 observed under competitive mating conditions may have potential
 ramifications for male and female reproductive success, and discuss how
 patterns of selection acting on male body size might limit the extent of
 SSD in this species.