cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s9n91
title: Data from: Ditch network sustains functional connectivity and influences patterns of gene flow in an intensive agricultural landscape

description: In intensive agricultural landscapes, plant species previously relying on
 semi-natural habitats may persist as metapopulations within landscape
 linear elements. Maintenance of populations’ connectivity through pollen
 and seed dispersal is a key factor in species persistence in the face of
 substantial habitat loss. The goals of this study were to investigate the
 potential corridor role of ditches and to identify the landscape
 components that significantly impact patterns of gene flow among remnant
 populations. Using microsatellite loci, we explored the spatial genetic
 structure of two hydrochorous wetland plants exhibiting contrasting local
 abundance and different habitat requirements: the rare and regionally
 protected Oenanthe aquatica and the more commonly distributed Lycopus
 europaeus, in an 83 km2 agricultural lowland located in northern France.
 Both species exhibited a significant spatial genetic structure, along with
 substantial levels of genetic differentiation, especially for L.
 europaeus, which also expressed high levels of inbreeding.
 Isolation-by-distance analysis revealed enhanced gene flow along ditches,
 indicating their key role in effective seed and pollen dispersal. Our data
 also suggested that the configuration of the ditch network and the
 landscape elements significantly affected population genetic structure,
 with (i) species-specific scale effects on the genetic neighborhood and
 (ii) detrimental impact of human ditch management on genetic diversity,
 especially for O. aquatica. Altogether, these findings highlighted the key
 role of ditches in the maintenance of plant biodiversity in intensive
 agricultural landscapes with few remnant wetland habitats.
description: Coordinates of sample
 locations and genotype data for two species : Lycopus europeus and
 Oenanthe aquaticaCoordinates (decimal
 degrees) and nuclear genetic data (microsatellite loci genotypes) for
 Oenanthe aquatica and Lycopus europeus species.Data-Favre-Bac et
 al.-HDY-14-OR0346RR .xls
DOI: 10.5061/dryad.k86m5
title: Data from: Are sexually selected traits affected by a poor environment early in life?

description: Background: Challenging conditions experienced early in life, such as a
 restricted diet, can detrimentally affect key life-history traits.
 Individuals can reduce these costs by delaying their sexual maturation,
 albeit at the price of the later onset of breeding, to eventually reach
 the same adult size as individuals that grow up in a benevolent
 environment. Delayed maturation can, however, still lead to other
 detrimental morphological and physiological changes that become apparent
 later in adulthood (e.g. shorter lifespan, faster senescence). In general,
 research focuses on the naturally selected costs of a poor early diet. In
 mosquitofish (Gambusia holbrooki), males with limited food intake early in
 life delay maturation to reach a similar adult body size to their well-fed
 counterparts (‘catch-up growth’). Here we tested whether a poor early diet
 is costly due to the reduced expression of sexually selected male
 characters, namely genital size and ejaculate traits. Results: We found
 that a male’s diet early in life significantly influenced his sperm
 reserves and sperm replenishment rate. Shortly after maturation males with
 a restricted early diet had significantly lower sperm reserves and slower
 replenishment rates than control diet males, but this dietary difference
 was no longer detectable in older males. Conclusions: Although delaying
 maturation to reach the same body size as well fed juveniles can
 ameliorate some costs of a poor start in life, our findings suggest that
 costs might still arise because of sexual selection against these males.
 It should be noted, however, that the observed effects are modest (Hedges’
 g = 0.20–0.36), and the assumption that lower sperm production translates
 into a decline in fitness under sperm competition remains unconfirmed.
description: Vega-Trejo et al. Sperm
 BMC- DataData from Are sexually
 selected traits affected by a poor environment early in life? by Regina
 Vega-Trejo, Michael D. Jennions and Megan L. Head. Excel file shows raw
 data on first spreadsheet and labels in the second one.
DOI: 10.5061/dryad.h3112
title: Data from: Historical dynamics of Batrachochytrium dendrobatidis in Amazonia

description: The Amazon forest is known for its astonishing amphibian diversity, yet
 the potential distribution and underlying impacts of the most important
 amphibian pathogen is unknown for most of Amazonia. In this retrospective
 survey of preserved Leptodactylus frogs, collected over a 119 yr period,
 we used quantitative PCR to detect the fungal pathogen Batrachochytrium
 dendrobatidis (Bd) and performed spatial scan analyses to identify
 spatiotemporal clusters of Bd. We also quantified the potential effect of
 environmental factors on the likelihood of Bd occurrence and generated an
 updated suitability map for Bd in the Amazon that included our
 retrospective sampling. We detected Bd in lowland Amazon as early as 1935,
 in the state of Pará, Brazil, and we found low prevalence (∼ 3.8%) over
 time. We identified two statistically significant spatiotemporal clusters
 of Bd: a recent and narrow cluster in the Amazon River delta and a
 spatiotemporally broad cluster in the southern edge of Amazon and
 Brazilian savanna. Furthermore, we found an increase in Bd-positive
 samples in the southwestern Amazon after the 1990s, coinciding with
 reported amphibian declines in neighboring high elevation sites on Andean
 slopes of Peru. Spatial regressions indicated that higher human
 interference, higher precipitation, and lower temperatures were
 significant predictors of Bd occurrence. Environmental niche modeling
 predicted some narrow areas of suitable climates along the Amazon's
 periphery and generally low climatic suitability for Bd in the central
 Amazon; although, we found clusters of Bd-positive samples with
 unexpectedly high infection loads in areas of predicted low suitability.
 Our study indicates that accelerated human development may put Amazonian
 amphibians at risk from Bd introductions, and it highlights the potential
 need to monitor Bd dynamics near Amazonian port cities.
description: Database-Bd-AmazonDatabase including geographic coordinates and pathogen infection status of Leptodactylus species collected during the last century in the Amazon forest.Database_Becker.xlsx
DOI: 10.5061/dryad.f6h25
title: Data from: How a generalist bee achieves high efficiency of pollen collection on diverse floral resources

description: Bees foraging for floral rewards are one of our most thoroughly studied
 examples of generalist foraging ecology. Generalist bees rely considerably
 on instrumental (associative) learning to acquire routines that allow them
 to collect nectar efficiently from diverse plant species. Although such
 bees must also collect pollen from diverse species, few studies have
 examined if and how high efficiency is achieved. We characterized how
 generalist bumble bees (Bombus impatiens) foraged effectively for pollen
 from diverse floral resources, by manipulating the presence of pollen and
 anther cues, in a series of experiments using pollen-bearing live flowers,
 flowers of a sterile pollenless horticultural hybrid, and artificial
 flowers. We show that generalist bumble bees exhibit flexible and
 effective pollen collection by switching between 2 routines: “scrabbling”
 when pollen is abundant and “sonicating” when pollen is scarce. Efficient
 switching between these behaviors is regulated by the interplay of 2
 ubiquitous floral cues: chemical anther cues stimulating pollen collection
 behavior and mechanical pollen cues suppressing sonication (and eliciting
 scrabbling). Flexible pollen collection behavior is functional: When
 pollen on anthers was scarce, bees collected it at a greater rate by
 sonicating than scrabbling. This mechanism of behavioral flexibility
 likely allows generalist bees to handle diverse anther morphologies
 efficiently and may have facilitated the recurrent evolution of plant
 species that conceal pollen rewards via pored floral morphology. Whereas
 effective nectar foraging relies heavily on associative learning of unique
 routines for each flower type, a weighing of 2 types of cues regulates the
 flexible pollen collection mechanism we describe.
description: Count data entered into
 ExcelCount data entered into
 Excel from handwritten data sheets. Ready for conversion into proportion
 data for analyses. Scanned data sheets (visit-by-visit data) are available
 upon request.Buzz elicitors ms data
 3-11-2017.zip
DOI: 10.15468/dl.k4pafw
title: Occurrence Download

description: A dataset containing 2439 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "CoordinateUncertaintyInMeters 0.0-500.0",
 "Country is one of (China, Chinese Taipei, Macao, Hong Kong, Philippines, United States of America, Japan, Northern Mariana Islands, Seychelles)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Acacia confusa",
 "Year 1980-2026"
 ]
}

 The dataset includes 2439 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000772-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d9n5d
title: Data from: Locomotor performance of cane toads differs between native-range and invasive populations

description: Invasive species provide a robust opportunity to evaluate how animals deal
 with novel environmental challenges. Shifts in locomotor performance—and
 thus the ability to disperse—(and especially, the degree to which it is
 constrained by thermal and hydric extremes) are of special importance,
 because they might affect the rate that an invader can spread. We studied
 cane toads (Rhinella marina) across a broad geographical range: two
 populations within the species' native range in Brazil, two invasive
 populations on the island of Hawai'i and eight invasive populations
 encompassing the eastern, western and southern limits of the toad invasion
 in Australia. A toad's locomotor performance on a circular raceway
 was strongly affected by both its temperature and its hydration state, but
 the nature and magnitude of those constraints differed across populations.
 In their native range, cane toads exhibited relatively low performance
 (even under optimal test conditions) and a rapid decrease in performance
 at lower temperatures and hydration levels. At the other extreme,
 performance was high in toads from southern Australia, and virtually
 unaffected by desiccation. Hawai'ian toads broadly resembled their
 Brazilian conspecifics, plausibly reflecting similar climatic conditions.
 The invasion of Australia has been accompanied by a dramatic enhancement
 in the toads' locomotor abilities, and (in some populations) by an
 ability to maintain locomotor performance even when the animal is cold
 and/or dehydrated. The geographical divergences in performance among cane
 toad populations graphically attest to the adaptability of invasive
 species in the face of novel abiotic challenges.
description: locomotor_canetodsRecords of distance ran by cane toads of different populations over 10 minutes on a circular track under different experimental conditions.locomotor_dryad.txt
DOI: 10.5061/dryad.1q9d0
title: Data from: Evolution mediates the effects of apex predation on aquatic food webs

description: Ecological and evolutionary mechanisms are increasingly thought to shape
 local community dynamics. Here, I evaluate if the local adaptation of a
 meso-predator to an apex predator alters local food webs. The marbled
 salamander (Ambystoma opacum) is an apex predator that consumes both the
 spotted salamander (Ambystoma maculatum) and shared zooplankton prey.
 Common garden experiments reveal that spotted salamander populations which
 co-occur with marbled salamanders forage more intensely than those that
 face other predator species. These foraging differences, in turn, alter
 the diversity, abundance and composition of zooplankton communities in
 common garden experiments and natural ponds. Locally adapted spotted
 salamanders exacerbate prey biomass declines associated with apex
 predation, but dampen the top-down effects of apex predation on prey
 diversity. Countergradient selection on foraging explains why locally
 adapted spotted salamanders exacerbate prey biomass declines. The two
 salamander species prefer different prey species, which explains why
 adapted spotted salamanders buffer changes in prey composition owing to
 apex predation. Results suggest that local adaptation can strongly mediate
 effects from apex predation on local food webs. Community ecologists might
 often need to consider the evolutionary history of populations to
 understand local diversity patterns, food web dynamics, resource gradients
 and their responses to disturbance.
description: Data from laboratory and
 mesocosm experiments and fieldFile includes data from
 mesocosm experiment, laboratory experiment, and field
 observationsUrban
 PrSB.xlsx
DOI: 10.5061/dryad.p614h
title: Data from: Resistance, tolerance and environmental transmission dynamics determine host extinction risk in a load-dependent amphibian disease

description: While disease-induced extinction is generally considered rare, a number of
 recently emerging infectious diseases with load-dependent pathology have
 led to extinction in wildlife populations. Transmission is a critical
 factor affecting disease-induced extinction, but the relative importance
 of transmission compared to load-dependent host resistance and tolerance
 is currently unknown. Using a combination of models and experiments on an
 amphibian species suffering extirpations from the fungal pathogen
 Batrachochytrium dendrobatidis (Bd), we show that while transmission from
 an environmental Bd reservoir increased the ability of Bd to invade an
 amphibian population and the extinction risk of that population,
 Bd-induced extinction dynamics were far more sensitive to host resistance
 and tolerance than to Bd transmission. We demonstrate that this is a
 general result for load-dependent pathogens, where non-linear resistance
 and tolerance functions can interact such that small changes in these
 functions lead to drastic changes in extinction dynamics.
description: Density-dependent
 transmission experiment for Rana muscosa and Bdformatted_dd_data.csv
DOI: 10.5061/dryad.0h2br0d
title: Data from: Can threatened species adapt in restored habitat? No expected evolutionary response in lay date for the New Zealand hihi

description: Many bird species have been observed shifting their laying date to earlier
 in the year in response to climate change. However the vast majority of
 these studies were performed on non-threatened species, less impacted by
 reduced genetic diversity (which is expected to limit evolutionary
 response) as a consequence of genetic bottlenecks, drift and population
 isolation. Here we study the relationship between lay date and fitness, as
 well as its genetic basis, to understand the evolutionary constraints on
 phenology faced by threatened species using a recently reintroduced
 population of the endangered New Zealand passerine, the hihi (Notiomystis
 cincta). A large discrepancy between the optimal laying date and the mode
 of laying date creates a strong selection differential of -11.24. The
 impact of this discrepancy on fitness is principally mediated through
 survival of offspring from hatchling to fledgling. This discrepancy does
 not seem to arise from a difference in female quality or a trade-off with
 lifetime breeding success. We find that start of breeding season depends
 on female age and average temperature prior to the breeding season. Laying
 date is not found to be significantly heritable. Overall, our research
 suggests that this discrepancy is a burden on hihi fitness, which will not
 be resolved through evolution or phenotypic plasticity. More generally,
 these results show that threatened species introduced to restored habitats
 might lack adaptive potential and plasticity to adjust their phenology to
 their new environment. This constraint is also likely to limit their
 ability to face future challenges, including climate change.
description: pedigreePedigree of the individuals contained in the dataset. First column contain the individuals id, second is the id of the mother ("dam") and third is the id of the (reconstructed with genetic data) father ("sire").dataPhenotypic and breeding data used in the articleBUGS modelModel used to estimate and analyse the optimum of laying date.model.bugPower analysis simulationsSimulations to analyse our power to estimate heritability.simulations.R
DOI: 10.5061/dryad.49d81
title: Data from: Wild dwarf mongooses produce general alert and predator-specific alarm calls

description: Many species produce alarm calls in response to predator threats. Whilst
 these can be general alert calls, some are urgency-based, indicating
 perceived threat level, some are predator-specific, indicating the
 predator type present, and some encode information about both urgency
 level and predator type. Predator-specific calls given to a narrow range
 of stimuli and which elicit a specific, adaptive, response from the
 receiver are termed functionally referential. Differing escape strategies,
 habitat structural complexity and sociality may favor the evolution of
 functionally referential calls. A study of one captive group of dwarf
 mongooses (Helogale parvula) suggested their alarm calls could transmit
 information about species, distance, and elevation of predators. Using
 recordings of natural predator encounters, predator presentations and
 audio playbacks, we investigated the alarm-call system in 7 wild dwarf
 mongoose groups. We recorded 11 different alarm-call types given to 9
 stimulus categories. Of the 5 commonly emitted alarm-call types, 3
 appeared to be non-specific and 2 predator-specific, given to aerial and
 terrestrial predators respectively. The remaining 6 call types were rarely
 produced. Furthermore, aerial alarms were given to a narrower range of
 stimuli than their terrestrial alarm calls, which were given to both
 visible terrestrial predators and secondary cues of predators. Unlike
 other mongoose species, dwarf mongoose seem to use the same alarm-call
 type for both physically present terrestrial predators and secondary cues
 of their presence. We argue that detailed knowledge of species’ alarm-call
 systems under natural conditions can shed light on the evolutionary
 emergence of different types of alarm calls.
description: Alarm-call-acoustic-parameters• Alarm-call-acoustic-parameters: Contains the values of the acoustic parameters measured for the different types of alarm calls.Alarm-calls-predator-presentations• Alarm-calls-predator-presentations: Gives the alarm call types produced in reaction to different types of predator presentations.Natural-Alarm-calls• Natural-Alarm-calls: Lists the different alarm calls recorded during natural encounters with the putative referent they were given to and the type of call they were classed as.Playbacks• Playbacks: Gives the identity of focal mongooses used for playbacks and their responses to the playback of different type of call. (DM: dominant male; DF: dominant female; SM: subordinate male; SF: subordinate female)Reactions-natural-alarm-calls• Reactions-natural-alarm-calls: Lists the responses of mongooses when hearing an alarm produced in response to a natural predator encounter.
DOI: 10.5061/dryad.7q523
title: Data from: Getting there and around: host range oscillations during colonisation of the Canary Islands by the parasitic nematode Spauligodon

description: Episodes of expansion and isolation in geographic range over space and
 time, during which parasites have the opportunity to expand their host
 range, are linked to the development of host-parasite mosaic assemblages
 and parasite diversification. In this study we investigated whether island
 colonisation events lead to host range oscillations in a taxon of
 host-specific parasitic nematodes of the genus Spauligodon in the Canary
 Islands. We further investigated if range oscillations also resulted in
 shifts in host breadth (i.e. specialization), as expected for parasites on
 islands. Parasite phylogeny and divergence time estimates were inferred
 from molecular data with Bayesian methods. Host divergence times were set
 as calibration priors after a priori evaluation with a global-fit method
 of which individual host-parasite associations likely represent
 cospeciation links. Parasite colonisation history was reconstructed,
 followed by an estimation of oscillation events and specificity level. The
 results indicate the presence of four Spauligodon clades in the Canary
 Islands, which originated from at least three different colonisation
 events. We found evidence of host range oscillations to truly novel hosts,
 which in one case led to higher diversification. Contemporary
 host-parasite associations show strong host specificity, suggesting that
 changes in host breadth were limited to the shift period. Lineages with
 more frequent and wider taxonomic host range oscillations prior to the
 initial colonisation event showed wider range oscillations during
 colonisation and diversification within the archipelago. Our results
 suggest that a lineage’s evolutionary past may be the best indicator of a
 parasite’s potential for future range expansions.
description: BEAST input
 filexml file for the
 divergence time estimates with the three calibration
 priorsall123.1.xmlPACoDATAInput data used in the cophylogenetic analysis using the global-fit statistic tool PACo.
DOI: 10.5061/dryad.640j4
title: Data from: Divergent evolution peaks under intermediate population bottlenecks during bacterial experimental evolution

description: There is growing evidence that parallel molecular evolution is common, but
 its causes remain poorly understood. Demographic parameters such as
 population bottlenecks are predicted to be major determinants of
 parallelism. Here, we test the hypothesis that bottleneck intensity shapes
 parallel evolution by elucidating the genomic basis of adaptation to
 antibiotic-supplemented media in hundreds of populations of the bacterium
 Pseudomonas fluorescens Pf0-1. As expected, bottlenecking decreased the
 rate of phenotypic and molecular adaptation. Surprisingly, bottlenecking
 had no impact on the likelihood of parallel adaptive molecular evolution
 at a genome-wide scale. However, bottlenecking had a profound impact on
 the genes involved in antibiotic resistance. Specifically, under either
 intense or weak bottlenecking, resistance predominantly evolved by
 strongly beneficial mutations which provide high levels of antibiotic
 resistance. In contrast with intermediate bottlenecking regimes,
 resistance evolved by a greater diversity of genetic mechanisms,
 significantly reducing the observed levels of parallel genetic evolution.
 Our results demonstrate that population bottlenecking can be a major
 predictor of parallel evolution, but precisely how may be more complex
 than many simple theoretical predictions.
description: Vogwill et al Proc B
 divergent evolution and bottlenecksGrowth rates and
 mutation data for Vogwill et al (divergent evolution and bottlenecks). Tab
 1 contains growth rates, tab 2 contains the identified mutations for each
 clone.Vogwill Phillips Gifford
 Maclean Data.xlsx