cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.47d7wm38h
title: Population history explains the performance of an annual herb - within and beyond its European species range

description: 1. The centre-periphery hypothesis (CPH) predicts a decrease in population
 performance from the centre of the species range towards the edge,
 hindering further species expansion. To overcome ecological limitation,
 local adaptation of peripheral populations is assumed necessary to extend
 niche space and thus to potentially facilitate species’ range expansion.
 However, adaptive changes do not necessarily correspond to current
 ecological marginality. Instead, population history may provide a fuller
 context for understanding patterns of local adaptation within the species
 range. Here, we test whether local adaptation to current conditions or
 population history explains current species distribution in an annual
 heterocarpic species, Atriplex tatarica, in Europe. 2. The ecological
 marginality and population history were estimated using species
 distribution modelling (SDM) and 13 microsatellite markers. To test for
 local adaptation, we evaluated the population performance of both
 currently central and currently peripheral populations by examining
 germination and growth traits under three temperature regimes which
 correspond to climates within, and also beyond, the species’ current
 range. In addition, we compared Bayesian estimates of population
 differentiation in neutral genetic markers and quantitative traits to test
 whether phenotypic differentiation evolved by local adaptation and/or by
 genetic drift. 3. We found population performances were not higher under
 temperature regimes corresponding to their own habitats, suggesting that
 patterns of local adaptation in A. tatarica do not correspond to current
 centre-periphery gradient. In contrast, population genetic structure
 indicated a strong influence of population history on variation in the
 germination phenotype. Species distribution modelling suggested a more
 cold-tolerant genetic lineage was located at the species’ range periphery
 during the last glacial period. Meanwhile, a less cold-tolerant lineage
 occurred in more suitable areas of the Balkan Peninsula and southeastern
 Europe. Thus, the strong adaptive divergence of evolutionary lineages may
 reflect a past spatial arrangement of populations, suggesting evolutionary
 processes were ongoing before the species expansion in the Holocene. 4.
 Synthesis. There is continuing debate concerning the speed of trait
 evolution during range expansion with climate change. Our results indicate
 that even though organisms expand rapidly, the accompanying evolutionary
 changes in phenotype may be much slower.
DOI: 10.5061/dryad.08kprr4xz
title: Ancient mitogenomics clarifies radiation of extinct Mascarene giant tortoises (Cylindraspis spp.)

description: The five extinct giant tortoises of the genus Cylindraspis belong to the
 most iconic species of the enigmatic fauna of the Mascarene Islands that
 went largely extinct after the discovery of the islands. To resolve the
 phylogeny and biogeography of Cylindraspis, we analysed a data set of 45
 mitogenomes that includes all lineages of extant tortoises and eight
 near-complete sequences of all Mascarene species extracted from historic
 and subfossil material. Cylindraspis is an ancient lineage that diverged
 as early as the late Eocene. Diversification of Cylindraspis commenced in
 the mid-Oligocene, long before the formation of the Mascarene Islands.
 This rejects any notion suggesting that the group either arrived from
 nearby or distant continents over the course of the last millions of years
 or had even been translocated to the islands by humans. Instead,
 Cylindraspis likely originated on now submerged islands of the Réunion
 Hotspot and utilized these to island hop to reach the Mascarenes. The
 final diversification took place both before and after the arrival on the
 Mascarenes. With Cylindraspis a deeply divergent clade of tortoises became
 extinct that evolved long before the dodo or the Rodrigues solitaire, two
 other charismatic species of the lost Mascarene fauna.
description: (1) BioGeoBEARS data matrix and DIVALIKE results
 (2) Alignments
DOI: 10.5061/dryad.bnzs7h469
title: Urban herring gulls use human behavioural cues to locate food

description: While many animals are negatively affected by urbanisation, some species
 appear to thrive in urban environments. Herring gulls (Larus argentatus)
 are commonly found in urban areas and often scavenge food discarded by
 humans. Despite increasing interactions between humans and gulls, little
 is known about the cognitive underpinnings of urban gull behaviour and to
 what extent they use human behavioural cues when making foraging
 decisions. We investigated whether gulls are more attracted to
 anthropogenic items when they have been handled by a human. We first
 presented free-living gulls with two identical food objects, one of which
 was handled, and found that gulls preferentially pecked at the handled
 food object. We then tested whether gulls’ attraction to human-handled
 objects generalises to non-food items by presenting a new sample of gulls
 with two non-food objects, where, again, only one was handled. While
 similar numbers of gulls approached food and non-food objects in both
 experiments, they did not peck at handled non-food objects above chance
 levels. These results suggest that urban gulls generally show low levels
 of neophobia, but that they use human handling as a cue specifically in
 the context of food. These behaviours may contribute to gulls’ successful
 exploitation of urban environments.
DOI: 10.5061/dryad.8cz8w9gkn
title: Costs and benefits of multiple mating in a species with first male sperm precedence

description: 1. Different patterns of sperm precedence are expected to entail different
 costs and benefits of mating for each sex that translate into distinct
 predictions regarding mating system evolution. Still, most studies
 addressing these costs and benefits have focused on species with mixed
 paternity or last male precedence, neglecting first male sperm precedence.
 We attempted to understand whether this latter pattern of sperm precedence
 translates into different costs and benefits for each sex in the
 haplodiploid spider mite Tetranychus urticae, a species in which female
 multiple mating is prevalent but the majority of the offspring is sired by
 first males. 2. First, we assessed the stability of the sperm precedence
 pattern. To do so, we measured offspring paternity after exposing females
 to a different number of matings and mating intervals. Next, to determine
 the potential costs or benefits of multiple mating for females under
 different contexts, we measured the fecundity and survival of females that
 re-mated at different time points. To measure the potential costs of
 multiple mating for males, we analysed male survival in the presence of
 different numbers of virgin or mated females. We also tested whether males
 can reduce offspring production of their competitors, by reducing the
 production of fertilized offspring of mated females. 3. We found no change
 in the pattern of sperm precedence, independently of the mating interval
 between matings and the number of matings. Females paid a cost of mating,
 as multiply mated females laid fewer eggs than once-mated females.
 However, while males had reduced survival when exposed to an intermediate
 number of virgin females, they paid no additional costs of mating with
 mated females. Moreover, females that mated multiple times produced fewer
 fertilized offspring than females that mated once. Thus, males that
 copulated with mated females reduced the fitness of other males,
 potentially leading to a relative fitness benefit for themselves. 4. Our
 results show that complex costs and benefits may arise in males in species
 with first male sperm precedence. How these costs and benefits affect the
 maintenance of selection for polyandry remains an open question.
 29-Nov-2019
DOI: 10.5061/dryad.xksn02vbh
title: Hybridization between Felis silvestris silvestris and Felis silvestris catus in two contrasted environments in France

description: European wildcat (Felis silvestris silvestris) populations are fragmented
 throughout most of the whole range of the sub-species, and may be
 threatened by hybridization with the domestic cat F.s. catus. The
 underlying ecological processes promoting hybridization, remain largely
 unknown. In France, wildcats are mainly present in the North-East and
 signs of their presence in the Pyrenees have been recently provided.
 However, no studies have been carried out in the French Pyrenees to assess
 their exposure to hybridization. We compared two local populations of
 wildcats, one living in a continuous forest habitat in the French
 Pyrenees, the other living in a highly fragmented forest-agricultural
 landscape in Northeastern France to get insights into the variability of
 hybridization rates. Strong evidence of hybridization was detected in
 Northeastern France and not in the Pyrenees. Close kin in the Pyrenees
 were not found in the same geographic location contrary to what was
 previously reported for females in the Northeastern wildcat population.
 The two wildcat populations were significantly differentiated (Fst =
 0.072) to an extent close to what has been reported (Fst = 0.103) between
 the Iberian population, from which the Pyrenean population may originate,
 and the German population, which is connected to the Northeastern
 population. The genetic diversity of the Pyrenean wildcats was lower than
 that of Northeastern wildcat populations in France and in other parts of
 Europe. The lower hybridization in the Pyrenees may result from the
 continuity of natural forest habitats. Further investigations should focus
 on linking landscape features to hybridization rates working on local
 populations.
DOI: 10.5061/dryad.w9ghx3fk0
title: Accuracy of identifying incident stroke cases from linked healthcare data in UK Biobank

description: Objective: In UK Biobank (UKB), a large population-based prospective
 study, cases of many diseases are ascertained through linkage to routinely
 collected, coded national health datasets. We assessed the accuracy of
 these for identifying incident strokes. Methods: In a regional UKB
 sub-population (n=17,249), we identified all participants with ≥1 code
 signifying a first stroke after recruitment (incident stroke-coded cases)
 in linked hospital admission, primary care or death record data. Stroke
 physicians reviewed their full electronic patient records (EPRs) and
 generated reference standard diagnoses. We evaluated the number and
 proportion of cases that were true positives (i.e. positive predictive
 value, PPV) for all codes combined and by code source and type. Results:
 Of 232 incident stroke-coded cases, 97% had EPR information available.
 Data sources were: 30% hospital admission only; 39% primary care only; 28%
 hospital and primary care; 3% death records only. While 42% of cases were
 coded as unspecified stroke type, review of EPRs enabled a pathological
 type to be assigned in &gt;99%. PPVs (95% confidence intervals) were:
 79% (73%-84%) for any stroke (89% for hospital admission codes, 80% for
 primary care codes) and 83% (74%-90%) for ischemic stroke. PPVs for small
 numbers of death record and hemorrhagic stroke codes were low but
 imprecise.  Conclusions: Stroke and ischemic stroke cases in UKB
 can be ascertained through linked health datasets with sufficient accuracy
 for many research studies. Further work is needed to understand the
 accuracy of death record and hemorrhagic stroke codes and to develop
 scalable approaches for better identifying stroke types.
description: <b>Supplementary Figure S1: </b>Pathway for code
 assignment and linkages in UK Biobank 
 <b>Supplementary Figure S2</b>: Code sources (a) and
 proportion of cases with codes for unspecified versus specified stroke
 type (b)  <b>Supplementary Figure S3</b>:
 Stroke type and subtype distributions 
 <b>Supplementary Table S1</b>: ICD10 and Read v2
 stroke codes  <b>Appendix 1:
 </b>Questionnaire for stroke outcome adjudication
DOI: 10.5061/dryad.280gb5mmf
title: Statistical prediction of the future impairs episodic encoding of the present

description: The following submission contains the behavioral data reported from the
 manuscript "Statistical prediction of the future impairs episodic
 encoding of the present". Data from four experiments are included.
 All experiments contained a learning phase, in which participants
 viewed a series of trial-unique scenes drawn from one of 12 scene
 categories and were asked to report whether or not the on-screen scene
 contained a manmade object. Accuracy and response time were measured
 during this task. Each scene category belonged to one of three conditions:
 A scenes, which were predictive of B scenes (which were thus predictable),
 and X scenes which could be preceded or followed by any number of scene
 categories and thus were neither predictive nor predictable. All
 experiments also contained a memory phase, in which participants were
 shown a scene image and were asked to indicate whether or not that
 particular scene image was presented in the learning phase. All scenes
 from the learning phase, in addition to a subset of images that were not
 presented during the learning phase (foils) were presented during the
 memory phase. After indicating whether an image was old or new,
 participants then indicated their confidence in their response
 (Experiments 1a, 1b & 3) or when in time they remember
 seeing the image (Experiment 2; old responses only). Experiments 1a
 & 2 additionally contained a category pair test. On each trial,
 participants were presented with two pairs of images and were
 asked to indicate which pair felt more familiar to them. Trials consisted
 either of a true A/B pair and a scrambled A/B pair (for which a trial
 would be accurate if participants chose the true A/B pair), or two
 dummy-coded X/X pairs (to which there was no objectively correct
 answer). 
description: See attached README.txt for additional information.
DOI: 10.5061/dryad.3n5tb2rcj
title: Data from: Contribution of European forests to safeguard wild honey bee populations

description: Recent studies reveal the use of tree cavities by wild honey bee colonies
 in European forests. This highlights the conservation potential of forests
 for a highly threatened component of the native entomofauna in Europe, but
 currently no estimate of potential wild honey bee population sizes exists.
 Here, we analysed the tree cavity densities of 106 forest areas across
 Europe and inferred an expected population size of wild honey bees. Both
 forest and management types affected the density of tree cavities.
 Accordingly, we estimated that more than 80,000 wild honey bee colonies
 could be sustained in European forests. As expected, potential
 conservation hotspots were identified in unmanaged forests, and,
 surprisingly, also in other large forest areas across Europe. Our results
 contribute to the EU policy strategy to halt pollinator declines and
 reveal the potential of forest areas for the conservation of so far
 neglected wild honey bee populations in Europe.
DOI: 10.5061/dryad.3tx95x6bm
title: Migratory lineages rapidly evolve larger body sizes than non-migratory relatives in ray-finned fishes

description: Migratory animals respond to environmental heterogeneity by predictably
 moving long distances in their lifetime. Migration has evolved repeatedly
 in animals, and many adaptations are found across the tree of life that
 increase migration efficiency. Life history theory predicts that migratory
 species should evolve a larger body size than non-migratory species and
 some empirical studies have shown this pattern. A recent study analyzed
 the evolution of body size between diadromous and non-diadromous shads,
 herrings, anchovies and allies, finding that species evolved larger body
 sizes when adapting to a diadromous lifestyle.  It remains
 unknown whether different fish clades adapt to migration similarly.
  We used an adaptive landscape framework to explore body size
 evolution for over 4500 migratory and non-migratory species of ray-finned
 fishes. By fitting models of macroevolution, we show that migratory
 species are evolving towards a body size that is larger than non-migratory
 species. Furthermore, we find that migratory lineages evolve towards their
 optimal body size more rapidly than non-migratory lineages, indicating
 body size is a key adaption for migratory fishes. Our results show, for
 the first time, that the largest vertebrate radiation on the planet
 exhibited strong evolutionary determinism when adapting to a migratory
 lifestyle.
DOI: 10.5061/dryad.bg79cnp76
title: Evasion of plant innate defense response by Salmonella on Lettuce

description: To establish host association, the innate immune system, which is one of
 the first lines of defense against infectious disease, must be
 circumvented. Plants encounter enteric foodborne bacterial pathogens under
 both pre- and post-harvest conditions. Human enteric foodborne pathogens
 can use plants as temporary hosts. This unique interaction may result in
 recalls and illness outbreaks associated with raw agricultural
 commodities. The purpose of this study was to determine if Salmonella
 enterica Typhimurium applied to lettuce leaves can suppress the innate
 stomatal defense in lettuce and utilization of  Bacillus subtilis
 strain UD1022 as a biocontrol against this ingression. Lettuce leaves were
 spot inoculated with S. Typhimurium wild type and its mutants. Bacterial
 culture and confocal microscopy analysis of stomatal apertures were used
 to support findings of differences in S. Typhimurium mutants compared to
 wild type. The persistence and internalization of these strains on lettuce
 was compared over a seven-day trial. S. Typhimurium may bypass the innate
 stomatal closure defense response in lettuce. Interestingly, a few key
 T3SS components in S. Typhimurium were involved in overriding stomatal
 defense response in lettuce for ingression. We also show that the T3SS in
 S. Typhimurium plays a critical role in persistence of S. Typhimurium in
 planta.  Salmonella populations were significantly reduced in all
 UD1022 groups by day seven with the exception of fliB and invA mutants.
 Salmonella internalization was not detected in plants after UD1022
 treatment and had significantly higher stomatal closure rates (aperture
 width=2.34µm) by day 1 compared to controls (8.5 µm). S. Typhimurium SPI1
 and SPI2 mutants showed inability to reopen stomates in lettuce suggesting
 the involvement of key T3SS components in suppression of innate response
 in plants. These findings impact issues of contamination related to plant
 performance and innate defense responses for plants.
description: Data was gathered using confocal microscopy and propiudium iodide
 staining of stomatal guard cells for quantification of stomatal aperture
 in relation tot he induction and strength of pattern triggered immunty and
 the plant innate defese responses to food borne pathogens.  excel
 spreadsheets include only the stomatal aperture measurements in microns.
 closed stomatal recieved a measurement of 0 and is recorded in that
 way.  semquanitative gene expression were gathered on
 several abscisic acid genes. plate counts and MPN
 emthdos were used for calculating the ability of food borne pathogens to
 persist on plants grown in both hydroponic, soilles media with and without
 addition of a benefical root microbe "plant growth promoting
 rhizobacteria"     data was proccessed using
 Microsoft Excel, Image J open sources image analysis software, and
 math. 
description: Micrographs gathered with confocal microsocpy were in excess
 of 10 GB/ 300GB and cannot be  uploaded to this data sharing
 service.
DOI: 10.5061/dryad.59zw3r23g
title: Trophic structure and mercury transfer in the subarctic fish community of Great Slave Lake, Northwest Territories, Canada

description: In recent decades, mercury concentrations have increased in fish of Great
 Slave Lake (GSL), a subarctic great lake in northern Canada with important
 recreational, subsistence, and commercial fisheries. This study
 characterized habitat use and trophic position of common fish species in
 GSL near the City of Yellowknife (Northwest Territories, Canada), measured
 mercury concentrations in water and in taxa from lower trophic levels of
 the food web, and examined trophic and biological influences on mercury
 concentrations within and among fish species. Northern pike (Exos lucius)
 and lake whitefish (Coregonus clupeformis) fed predominantly nearshore,
 cisco (Coregonus artedi) and longnose sucker (Catostomus catostomus) fed
 predominantly offshore, and burbot (Lota lota) fed roughly equally in both
 habitats. Habitat-specific feeding did not influence mercury
 bioaccumulation in fish, in contrast with published studies of smaller
 lakes. Water concentrations of total mercury and methylmercury were low
 and showed little spatial variation among sites or depths. Zooplankton
 (&gt;200 µm) had similarly low methylmercury concentrations to
 littoral and profundal amphipods, suggesting little habitat-variation of
 mercury exposure near the base of the food web. Age, size, and trophic
 position were significant explanatory variables for muscle total mercury
 concentrations within populations of fish species. Among fish species,
 size and trophic position explained 80% of the variation in muscle total
 mercury concentrations. This study generated the most comprehensive
 dataset to date on mercury bioaccumulation in the food web of GSL, which
 will serve as a baseline for future studies of this great lake.
description: Please refer to the manuscript for all methodological details or
 contact the corresponding author (john.chetelat@canada.ca) for more
 information. Rohonczy, J.; Cott, P. A.;
 Benwell, A.; Forbes, M. R.; Robinson, S. A.; Rosabal, M.; Amyot, M.;
 Chételat, J., Trophic structure and mercury transfer in the subarctic fish
 community of Great Slave Lake, Northwest Territories, Canada.
 <i>Journal of Great Lakes Research
 </i><b>2020,</b> <i>46</i>, (2), 402-413.
DOI: 10.5061/dryad.cnp5hqc1g
title: Maternal predation risk increases offspring’s exploration but does not affect schooling behavior

description: The environment that parents experience can influence their reproductive
 output and their offspring’s fitness via parental effects. Perceived
 predation risk can affect both parent and offspring phenotype, but it
 remains unclear to what extent offspring behavioral traits are affected
 when the mother is exposed to predation risk. This is particularly unclear
 in live-bearing species where maternal effects could occur during
 embryogenesis. Here, using a half-sib design to control for paternal
 effects, we experimentally exposed females of a live-bearing fish, the
 guppy (Poecilia reticulata), to visual predator cues and conspecific alarm
 cues during their gestation. Females exposed to predation risk cues
 increased their anti-predator behaviors throughout the entire treatment.
 Offspring of mothers exposed to the predation stimuli exhibited more
 pronounced exploratory behavior, but did not show any significant
 differences in their schooling behavior, compared to controls. Thus, while
 maternally perceived risk affected offspring’s exploration during early
 stages of life, offspring’s schooling behavior could be influenced more by
 direct environmental experience, rather than via maternal cues. Our
 results suggest a rather limited role in predator-induced maternal effects
 on the behavior of juvenile guppies.