cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bnzs7h47c
title: Data from: Skull morphology diverges between urban and rural populations of red foxes mirroring patterns of domestication and macroevolution

description: Human activity is drastically altering the habitat use of natural
 populations. This has been documented as a driver of phenotypic divergence
 in a number of wild animal populations. Here we show that urban and rural
 populations of red foxes (Vulpes vulpes) from London and surrounding
 boroughs are divergent in skull traits. These changes are primarily found
 to be involved with snout length, with urban individuals tending to have
 shorter and wider muzzles relative to rural individuals, smaller
 braincases, and reduced sexual dimorphism. Changes were widespread and
 related to muscle attachment sites and thus are likely driven by differing
 biomechanical demands of feeding or cognition between habitats. Through
 extensive sampling of the genus Vulpes, we found no support for
 phylogenetic effects on skull morphology, but patterns of divergence found
 between urban and rural habitats in V. vulpes quantitatively aligned with
 macroevolutionary divergence between species. The patterns of skull
 divergence between urban and rural habitats matched the description of
 morphological changes that can occur during domestication. Specifically,
 urban populations of foxes show variation consistent with ‘domestication
 syndrome’. Therefore, we suggest that occurrences of phenotypic divergence
 in relation to human activity, while interesting themselves, also have the
 potential to inform us of the conditions and mechanisms that could
 initiate domestication. Finally, this also suggests that patterns of
 domestication may be developmentally biased toward larger patterns of
 interspecific divergence.
description: The data was collected from museum samples in the UK. Details are
 provided in the primary manuscript. 
description: All data is provided, please contact the corresponding author for
 any questions
DOI: 10.5061/dryad.r2280gb9s
title: Cephalic biomechanics underpins the evolutionary success of trilobites

description: Arthropods (i.e. insects, spiders, crustaceans, myriapods and others), are
 the most successful Phanerozoic animals. The group are characterised by
 the possession of a segmented body, jointed limbs and a hard cuticle that
 is episodically moulted. One highly successful, but now extinct, group of
 arthropods are the trilobites. Trilobites underwent episodic moulting
 (ecdysis), and most trilobites possess facial sutures, lines of weakness
 in the cephalon, via which the exuviae is shed and the animal emerges.
 However, zones of weakness appear to represent a structural trade-off or
 constraint, particularly during burrowing behaviours; sacrificing a
 consolidated head region useful in burrowing for the ability to moult.
 Here we reconcile this trade-off by using biomechanical modelling to
 demonstrate that facial sutures exist in regions of low stress during the
 application of burrowing loads. Furthermore, facial sutures and the
 structure of the cephalon enable sutured trilobites to withstand greater
 stresses than their non-suture counterparts. We suggest that this ability
 to withstand greater burrowing loads enabled trilobites to successfully
 invade bioturbated and more consolidated sediments of the Cambrian
 Sediment Revolution, thus facilitating their diversification in the
 Cambrian and Ordovician and contributing to the evolutionary success of
 this iconic arthropod group.
DOI: 10.5061/dryad.sj3tx9629
title: Data from: Drought mildly reduces plant dominance in a temperate prairie ecosystem across years

description: 1. Shifts in dominance and species reordering can occur in response to
 global change. However, it is not clear how altered precipitation and
 disturbance regimes interact to affect species composition and dominance.
 2. We explored community-level diversity and compositional similarity
 responses, both across and within years, to a manipulated precipitation
 gradient and annual clipping in a mixed-grass prairie in Oklahoma, USA. We
 imposed seven precipitation treatments (five water exclusion levels [-20%,
 -40%, -60%, -80%, and -100%], water addition [+50%], and control [0%
 change in precipitation]) year-round from 2016-2018 using fixed
 interception shelters. These treatments were crossed with annual clipping
 to mimic hay harvest. 3. We found that community-level responses were
 influenced by precipitation across time. For instance, plant evenness was
 enhanced by extreme drought treatments, while plant richness was
 marginally promoted under increased precipitation. 4. Clipping promoted
 species gain resulting in greater richness within each experimental year.
 Across years, clipping effects further reduced the precipitation effects
 on community-level responses (richness and evenness) at both extreme
 drought and added precipitation treatments. 5. Synthesis: Our results
 highlight the importance of studying interactive drivers of change both
 within vs. across time. For instance, clipping attenuated community-level
 responses to a gradient in precipitation, suggesting that management could
 buffer community-level responses to drought. However, precipitation
 effects were mild and likely to accentuate over time to produce further
 community change.
DOI: 10.5061/dryad.dz08kprv7
title: Prior exposure to long day photoperiods alters immune responses and increases susceptibility to parasitic infection in stickleback

description: Seasonal disease and parasitic infection are common across organisms,
 including humans, and there is increasing evidence for intrinsic seasonal
 variation in immune systems. Changes are orchestrated through organisms’
 physiological clocks using cues such as day length. Ample research in
 diverse taxa has demonstrated multiple immune responses are modulated by
 photoperiod, but to date, there have been few experimental demonstrations
 that photoperiod cues alter susceptibility to infection. We investigated
 the interactions among photoperiod history, immunity, and susceptibility
 in laboratory-bred three-spined stickleback, a long-day breeding fish, and
 its external, directly-reproducing, monogenean parasite Gyrodactylus
 gasterostei. We demonstrate that previous exposure to long day
 photoperiods (PLD) increases susceptibility to infection relative to
 previous exposure to short days (PSD), and modifies the response to
 infection for the mucin gene muc2 and Treg cytokine foxp3a in skin tissues
 in an intermediate 12L:12D photoperiod experimental trial. Expression of
 skin muc2 is reduced in PLD fish, and negatively associated with parasite
 abundance. We also observe inflammatory gene expression variation
 associated with natural inter-population variation in resistance, but find
 that photoperiod modulation of susceptibility is consistent across host
 populations. Thus, photoperiod-modulation of the response to infection is
 important for host susceptibility, highlighting new mechanisms affecting
 seasonality of host-parasite interactions.
description: Data files: Infection16_Photo.csv
 - A dataset of photoperiods used to construct experimental
 timeline. Infection16_total_qPCR.csv - Relative
 expression data for all fish for which mRNA was sampled.
 Infection16_trackingweight.csv - Weight of fish tracked across
 the course of experiment. Infection16.csv -
 Biological sampling information for all sampling points for all
 fish. R code: 
 Infection16_Proc_submission.R - Analysis scripts for all
 analyses and figures 2-3 and S1-4.
 Infection16_functions.R - Generic functions used in
 analyses experimental_design_figure.R - Figure script
 for Figure 1.
DOI: 10.6078/d1597k
title: Data from: Predators can influence the host-parasite dynamics of their prey via non-consumptive effects

description: Ecological communities are partly structured by indirect interactions,
 where one species can indirectly affect another by altering its
 interactions with a third species. In the absence of direct predation,
 non-consumptive effects of predators on prey have important implications
 for subsequent community interactions. To better understand these
 interactions, we used a Daphnia-parasite-predator cue system to evaluate
 if predation risk affects Daphnia responses to a parasite. We investigated
 the effects of predator cues on two aspects of host-parasite interactions
 (susceptibility to infection and infection intensity), and whether or not
 these effects differed between sexes. Our results show that changes in
 response to predator cues caused an increase in the prevalence and
 intensity of parasite infections in female predator-exposed Daphnia.
 Importantly, the magnitude of infection risk depended on how long Daphnia
 were exposed to the cues. Additionally, heavily infected Daphnia that were
 constantly exposed to cues produced relatively more offspring. While males
 were ~5x less likely to become infected compared to females, we were
 unable to detect effects of predator cues on male Daphnia – parasite
 interactions. In sum, predators, prey, and their parasites can form
 complex subnetworks in food webs, necessitating a nuanced understanding of
 how non-consumptive effects may mediate these interactions.
DOI: 10.5061/dryad.x3ffbg7g2
title: Data from: Are you more than the sum of your parents’ genes? phenotypic plasticity in a clonal vertebrate and F1 hybrids of its parental species

description: All known vertebrate clones have originated from hybridization events and
 some have produced distinct evolutionary lineages via hybrid speciation.
 Amazon mollies (Poecilia formosa) present an excellent study system to
 investigate how clonal species have adapted to heterogeneous environments
 because they are the product of a single hybridization event between male
 sailfin mollies (P. latipinna) and female Atlantic mollies (P. mexicana).
 Here we ask whether the hybrid species differs from the combination of its
 parental species’ genes in its plastic response to different environments.
 Using a 3-way factorial design, we exposed neonates produced by Amazon
 mollies and reciprocal F1 hybrid crosses to different thermal (24° and 29°
 C) and salinity (0/2, 12, 20 ppt) regimes. We measured various ontogenetic
 and life history characteristics across the lifespan of females. Our major
 results were: 1) Reaction norms of growth and maturation to temperature
 and salinity are quite similar between the two hybrid crosses; 2) Amazon
 molly reaction norms were qualitatively different than the P.
 latipinna male and P. mexicana female (LxM)
 hybrids for the ontogenetic variables; 3) Amazon molly reaction norms in
 reproductive traits were also quite different from LxM hybrids; 4) The
 reaction norms of net fertility were very different between Amazon mollies
 and LxM hybrids. We conclude that best locale for Amazon mollies is not
 the best locale for hybrids, which suggests that Amazon mollies are not
 just an unmodified mix of parental genes but instead have adapted to the
 variable environments in which they are found.
DOI: 10.5061/dryad.5mkkwh730
title: Data from: Behavioral syndromes shape evolutionary trajectories via conserved genetic architecture

description: Behaviors are often correlated within broader syndromes, creating the
 potential for evolution in one behavior to drive evolutionary changes in
 other behaviors. Despite demonstrations that behavioral syndromes are
 common, this potential for evolutionary effects has not been demonstrated.
 Here we show that populations of field crickets (Gryllus integer) exhibit
 a genetically conserved behavioral syndrome structure, despite differences
 in average behaviors. We found that the distribution of genetic variation
 and genetic covariance among behavioral traits was consistent with genes
 and cellular mechanisms underpinning behavioral syndromes rather than
 correlated selection. Moreover, divergence among populations’ average
 behaviors was constrained by the genetically conserved behavioral
 syndrome. Our results demonstrate that a conserved genetic architecture
 linking behaviors has shaped the evolutionary trajectories of populations
 in disparate environments—illustrating an important way for behavioral
 syndromes to result in shared evolutionary fates.
description: Behavior of individual <em>Gryllus
 integer </em>crickets were measured and crickets bred according to a
 maternal & paternal half-sib design.
description: Please see associated github repository for code and rds files
 for MCMC outputs.  https://github.com/DochtermannLab/G-PopComparison
DOI: 10.5061/dryad.g79cnp5mp
title: Data from: Impact of brood parasitism and predation on nest survival of the fan-tailed gerygone in New Caledonia

description: Predation and brood parasitism are common reasons for nesting failure in
 passerine species and the additive impact by invasive species is a major
 conservation concern, particularly on tropical islands. Recognising the
 relative contribution of the different components of nesting failure rates
 is important to understand co-evolutionary interactions within brood
 parasite-host systems. In the remote archipelago of New Caledonia, the
 fan-tailed gerygone Gerygone flavolateralis is the exclusive host of the
 brood-parasitic shining bronze-cuckoo Chalcites lucidus. Additionally,
 invasive rodents also possibly have an impact on breeding success. To
 estimate the impact of potential nest predators, we 1) video monitored
 nests to identify predators, 2) estimated the probability of predation
 based on nest visibility and predator abundance and 3) tested the
 possibility that the location of experimental nests and lack of odour cues
 decrease the predation by rodents. In addition, we estimated nest survival
 rates using data collected in different habitats over the course of 8
 breeding seasons. Nesting success of fan-tailed gerygone was relatively
 low and predation was the main cause of nesting failure. We recorded
 mainly predation by native birds, including the shining bronze-cuckoo,
 whereas predation by rats was rare. In open habitats predation by cuckoos
 was much lower than predation by other avian predators. Neither predator
 activity around nests nor nest visibility influenced the probability of
 predation. Experimental nests in more accessible locations and containing
 an odorous bait were more exposed to rodent predation. Apparently, the
 fan-tailed gerygone has either never been specifically vulnerable to
 predation by rats or has developed anti-predator adaptations.
DOI: 10.5061/dryad.vx0k6djnv
title: Structural brain network abnormalities and the probability of seizure recurrence after epilepsy surgery: supplementary material

description: Objective: We assessed pre-operative structural brain networks and
 clinical characteristics of patients with drug resistant temporal lobe
 epilepsy (TLE) to identify correlates of post-surgical seizure
 recurrences. Methods: We examined data from 51 TLE patients who underwent
 anterior temporal lobe resection (ATLR) and 29 healthy controls. For each
 patient, using the preoperative structural, diffusion, and post-operative
 structural MRI, we generated two networks: ‘pre-surgery’ network and
 ‘surgically-spared’ network. Standardising these networks with respect to
 controls, we determined the number of abnormal nodes before surgery and
 expected to be spared by surgery. We incorporated these 2 abnormality
 measures and 13 commonly acquired clinical data from each patient in a
 robust machine learning framework to estimate patient-specific chances of
 seizures persisting after surgery.    Results:
 Patients with more abnormal nodes had lower chance of seizure freedom at 1
 year and even if seizure-free at 1 year, were more likely to relapse
 within five years. In the surgically-spared networks of poor outcome
 patients, the number of abnormal nodes was greater and their locations
 more widespread than in good outcome patients. We achieved 0.84±0.06 AUC
 and 0.89±0.09 specificity in predicting unsuccessful seizure outcomes as
 opposed to complete seizure freedom at 1-year. Moreover, the
 model-predicted likelihood of seizure relapse was significantly correlated
 with the grade of surgical outcome at year-one and associated with
 relapses up-to five years post-surgery. Conclusion: Node abnormality
 offers a personalised non-invasive marker, that can be combined with
 clinical data, to better estimate the chances of seizure freedom at 1
 year, and subsequent relapse up to 5 years after ATLR.
DOI: 10.5061/dryad.fbg79cns4
title: Data from: Genotyping-in-Thousands by sequencing reveals marked population structure in Western Rattlesnakes to inform conservation status

description: Delineation of units below the species level is critical for prioritizing
 conservation actions for species at-risk. Genetic studies play an
 important role in characterizing patterns of population connectivity and
 diversity to inform the designation of conservation units, especially for
 populations that are geographically isolated. The northernmost range
 margin of Western Rattlesnakes (Crotalus oreganus) occurs in British
 Columbia, Canada, where it is federally classified as threatened and
 restricted to five geographic regions. In these areas, Western
 Rattlesnakes hibernate (den) communally, raising questions about
 connectivity within and between den complexes. At present, Western
 Rattlesnake conservation efforts are hindered by a complete lack of
 information on genetic structure and degree of isolation at multiple
 scales, from the den to the regional level. To fill this knowledge gap, we
 used Genotyping-in-Thousands by sequencing (GT-seq) to genotype an
 optimized panel of 362 single nucleotide polymorphisms (SNPs) from
 individual samples (n = 461) collected across the snake’s distribution in
 western Canada and neighboring Washington (USA). Hierarchical STRUCTURE
 analyses found evidence for population structure within and among the five
 geographic regions in BC, as well as in Washington. Within these regions,
 11 genetically distinct complexes of dens were identified, with some
 regions having multiple complexes. No significant pattern of
 isolation-by-distance and generally low levels of migration were detected
 among den complexes across regions. Additionally, snakes within dens
 generally were more related than those among den complexes within a
 region, indicating limited movement. Overall, our results suggest that the
 single, recognized designatable unit for Western Rattlesnakes in Canada
 should be re-assessed to proactively focus conservation efforts on
 preserving total genetic variation detected range wide. More broadly, our
 study demonstrates a novel application of GT-seq for investigating
 patterns of diversity in wild populations at multiple scales to better
 inform conservation management.
description: GT-seq_308_488.vcf: vcf file containing genotypic data for 488
 Western rattlesnakes at 308 SNPs generated via GT-seq
 Metadata_488.xlsx: locality and sample information for 488
 Western rattlesnakes in British Columbia (Canada) and Washington
 (USA) Locus_info_362.csv: GT-seq genotyping input
 file
DOI: 10.15468/dl.vbfm5u
title: Occurrence Download

description: A dataset containing 171 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nyctiphanes australis",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 171 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002371-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.xksn02vc9
title: Bayesian tip-dated phylogenetics in paleontology: topological effects and stratigraphic fit

description: The incorporation of stratigraphic data into phylogenetic analysis has a
 long history of debate, but is not currently standard practice for
 paleontologists. Bayesian tip-dated (or morphological clock) phylogenetic
 methods have returned these arguments to the spotlight, but how tip dating
 affects the recovery of evolutionary relationships has yet to be fully
 explored. Here I show, through analysis of several datasets with multiple
 phylogenetic methods, that topologies produced by tip dating are outliers
 when compared to topologies produced by parsimony and undated Bayesian
 methods, which retrieve broadly similar trees. Unsurprisingly, trees
 recovered by tip dating have better fit to stratigraphy than trees
 recovered by other methods under both the Gap Excess Ratio and The
 Stratigraphic Completeness Index. This is because trees with better
 stratigraphic fit are assigned a higher likelihood by the fossilized
 birth-death tree model. However, the degree to which the tree model
 favours tree topologies with high stratigraphic fit metrics is modulated
 by the diversification dynamics of the group under investigation. In
 particular, when net diversification rate is low, the tree model favours
 trees with a higher Gap Excess Ratio compared to when net diversification
 rate is high. Differences in stratigraphic fit and tree topology between
 tip dating and other methods are concentrated in parts of the tree with
 weaker character signal, as shown by successive deletion of the most
 incomplete taxa from two datasets. These results show that tip dating
 incorporates stratigraphic data in an intuitive way, with good
 stratigraphic fit an expectation that can be overturned by strong evidence
 from character data.