cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2ngf1vhj1
title: Importance of intraspecific variation in the pollination and seed dispersal functions of a double mutualist animal species

description: Although most plants depend on different animals for pollination and seed
 dispersal, sometimes the same animal species provides both functions,
 being thus involved in what has been termed a ‘double mutualism’. Very
 little is known on the effectiveness of such species as both pollinators
 and seed dispersers, and even less on the intraspecific level differences
 at the contribution of an animal mutualist to plant fitness. In this
 study, we focused on the interaction between a Mediterranean shrub Cneorum
 tricoccon L. (Rutaceae) and the Balearic lizard Podarcis lilfordi L.
 (Lacertidae) in order to assess: (1) the role of this lizard as a
 legitimate pollinator of the plant (previously thought to be exclusively
 insect-pollinated), and (2) the intraspecific variation in the use of
 flowers and fruits by lizard individuals, comparing males, females and
 juveniles. We further evaluated whether lizards show different fruit size
 selection depending on sex and age, with potential consequences for seed
 germination. Lizards visited more flowers and selected more hermaphrodite
 flowers than insects did, leading to relative increases in both fruit and
 seed set. Interestingly, female and juvenile lizards were the main flower
 visitors, whereas males were the main fruit consumers. Males selected the
 largest fruits (bearing the largest seeds) though this did not increase
 seed germination, which was only ca. 15%. We concluded that P. lilfordi
 acts as a legitimate pollinator of C. tricoccon and, thus, confirm that
 this system constitutes a new case of double mutualism, especially common
 in island compared to mainland systems. Moreover, our findings show a
 large variation among conspecific individuals in their role as either
 pollinators or seed dispersers, with potential implications for plant
 reproductive success. Our study, therefore, highlights the importance of
 evaluating plant-animal interactions at the intraspecific level, and calls
 for more in-depth studies on the consequences of such intraspecific
 variation.
DOI: 10.5061/dryad.wpzgmsbgr
title: Data from: Development of flight and foraging behaviour in a juvenile seabird with extreme soaring capacities

description: 1) The early-life of animals is a period of high mortality, when foraging
 capacities are assumed to be improved progressively. In birds, this
 critical period involves the improvement of the flight. How do young birds
 gain these capacities has rarely been studied in natural conditions
 especially in seabirds that spend most of their life at sea. 2) We used
 detailed GPS and body acceleration data on 37 great frigatebirds (Fregata
 minor), to test the hypothesis that juveniles starting their first flights
 have lower flying capacities than adults, but that these capacities will
 improve during a long learning period, before independence from parents,
 specific to this seabird that can spend months on the wing at sea. 3) We
 found that most flight components improved over time to tend towards those
 of adults, especially the travel speed, range, duration and maximum
 altitude of trips. However, unexpectedly, juveniles had higher ascent
 rates, soaring and gliding capacities above the sea than adults. Moreover,
 energy expenditure of juveniles was similar to adults during low cost
 travelling movements and during active foraging, but juveniles spent more
 time foraging actively than adults. 4) Our results suggest that flight
 tactics based on long-distance effortless movements specific to this
 family are acquired during a long period, but soaring and gliding
 capacities are already inherited by juveniles and possibly favoured by
 morphological adaptations specific to juveniles. These adaptations might
 explain the extreme dispersive capacities of juveniles.
DOI: 10.5061/dryad.rjdfn2z5x
title: Data from: Comparative analysis of the multivariate genetic architecture of morphological traits in three species of Gomphocerine grasshoppers

description: Evolutionary change is the change in trait values across generations, and
 usually occurs in multidimensional trait space rather than along isolated
 traits. Genetic covariation influences the magnitude and direction of
 evolutionary change and can be statistically summarized by the additive
 genetic (co)variance matrix, G. While G can affect the response to
 selection, it is exposed to evolutionary change by selection and genetic
 drift, but the magnitude and speed of these changes are poorly understood.
 We use comparative G matrix analyses to assess evolution of the shape and
 orientation of G over longer time scales in three species of Gomphocerine
 grasshoppers. We estimate 10x10 G matrices for five morphological traits
 expressed in both sexes. We find low to moderate heritabilities (average
 0.36), mostly large cross-sex correlations (average 0.54) and moderate
 between-trait correlations (average 0.34). G matrices differ significantly
 among species with wing length contributing most to these differences.
 Wing length is the trait that is most divergent among species, suggesting
 it has been under selection during species divergence. The more distantly
 related species, Pseudochorthippus parallelus, was the most different in
 the shape of G. Projecting contemporary genetic variation into the
 divergence space D illustrates that the major axis of genetic variation in
 Gomphocerippus rufus is aligned with divergence from Chorthippus
 biguttulus, while the major axis of genetic variation in neither of the
 species is aligned with the divergence between Pseudochorthippus
 parallelus and the other two species. Our results demonstrate significant
 differences in G matrices with a phylogenetic signal in the
 differentiation.
description: This dataset consists of morphological measurements of three
 Gomphocerine grasshoppers, and their pedigree information. Of the three
 grasshoppers, <em>Chorthippus
 biguttulus </em>and <em>Pseudochorthippus
 parallelus </em>were collected from Bielefeld
 and <em>Gomphocerippus rufus </em>was collected from
 Tuebingen, in Germany. The measurements were taken from photographs with
 the help of the sofware ImageJ. The individuals used in the study come
 from a paternal half-sib breeding design set up in the lab with
 individuals caught from the field. 
description: There are three categories of files for each species,  a data
 file containing morphological measurements for the individuals used in the
 study, a pedigree file containing parental information, and ReadMe files
 which enlist the details of the data and pedigree files. There are missing
 values in the data as well as the pedigrees, and they are marked with
 NA.
DOI: 10.5061/dryad.qbzkh18cr
title: Phylotranscriptomic analyses reveal asymmetrical gene duplication dynamics and signatures of ancient polyploidy in mints

description: Ancient duplication events and retained gene duplicates have contributed
 to the evolution of many novel plant traits and, consequently, to the
 diversity and complexity within and across plant lineages. While mounting
 evidence highlights the importance whole-genome duplication (WGD;
 polyploidy) and its key role as an evolutionary driver, gene duplication
 dynamics and mechanisms, both of which are fundamental to our
 understanding of evolutionary process and patterns of plant diversity,
 remain poorly characterized in many clades. We use newly available
 transcriptomic data and a robust phylogeny to investigate the prevalence,
 occurrence, and timing of gene duplications in Lamiaceae (mints), a
 species-rich and chemically diverse clade with many ecologically,
 economically, and culturally important species. We also infer putative
 WGDs—an extreme mechanism of gene duplication—using large-scale data sets
 from synonymous divergence (KS), phylotranscriptomic, and divergence time
 analyses. We find evidence for widespread but asymmetrical levels of gene
 duplication and ancient polyploidy in Lamiaceae that correlate with
 species richness, including pronounced levels of gene duplication and
 putative ancient WGDs (7–18 events) within the large subclade Nepetoideae
 and up to 10 additional WGD events in other subclades. Our results help
 disentangle WGD-derived gene duplicates from those produced by other
 mechanisms and illustrate the non-uniformity of duplication dynamics in
 mints, setting the stage for future investigations that explore their
 impacts on trait diversity and species diversification. Our results also
 provide practical context for evaluating the benefits and limitations of
 transcriptome-based approaches to inferring WGD, and we offer
 recommendations for researchers interested in investigating ancient WGDs
 in other plant groups.
DOI: 10.5061/dryad.280gb5mm1
title: Data from: Population genetic structure and intraspecific genetic distance of Periplaneta americana (Blattodea: Blattidae) based on mitochondrial and nuclear DNA markers

description: The American cockroach (Periplaneta americana) is a globally invasive pest
 that can cause significant economic loss and threaten human health.
 Although it is abundant and lives in close proximity to humans, few
 studies have investigated the genetic diversity of P. americana. Our study
 analyzed 1053 P. americana and other Periplaneta species’ samples from
 different locations in China and the USA. A traditional tree-based method
 using 17 unique mitochondrial COI haplotypes of P. americana and 20
 haplotypes of the other Periplaneta species accurately identified P.
 americana with a barcoding threshold of 5.1%. To identify the population
 genetic structure of P. americana, we investigated wingless gene and
 pooled them with obtained mtDNA data for a combined analysis. Although the
 genetic diversity of the USA group was relatively higher than the China
 group, the number of haplotypes and alleles of both groups was small.
 Molecular variance (AMOVA), intraspecific phylogeny, and haplotype
 networks indicated that P. americana had very little global genetic
 differentiation. The weak geographic genetic structure might reflect the
 human-mediated dispersal of P. americana. Despite no apparent
 phylogeographic assignment of mtDNA and nuclear lineages was observed in
 both BI trees, the integrated COI sequence data identified four distinct
 P. americana haplotype groups, showing four ancient maternal lineages of
 P. americana in China and the USA.
DOI: 10.5061/dryad.7wm37pvnk
title: Unique bacterial assembly, composition, and interactions in a parasitic plant and its host

description: How plant-associated microbiota are shaped by, and potentially contribute
 to the unique ecology and heterotrophic life history of parasitic plants
 is relatively unknown. Here, we investigate the leaf and root bacterial
 communities associated with the root holoparasite Orobanche hederae and
 its host plant Hedera spp. We sequenced the V4 region of the 16S rRNA gene
 from DNA extracted from leaf and root samples of naturally growing
 populations of Orobanche and infected and uninfected Hedera. Root bacteria
 inhabiting Orobanche were less diverse, had fewer co-associations, and
 displayed increased compositional similarity to leaf bacteria relative to
 Hedera. Overall, Orobanche bacteria exhibited significant congruency with
 Hedera root bacteria across sites, but not the surrounding soil. Infection
 had localized and systemic effects on Hedera bacteria, which included
 effects on the abundance of individual taxa and root network properties.
 Collectively, our results indicate that the parasitic plant microbiome is
 derived but distinct from host plant microbiota, exhibits increased
 homogenization between shoot and root tissues, and displays far fewer
 co-associations among individual bacterial members. Host plant infection
 is accompanied by modest changes of associated microbiota at both local
 and systemic scales compared with uninfected individuals. The results are
 a first step towards extending the growing insight into the assembly and
 function of the plant microbiome to include the ecologically unique but
 often overlooked guild of heterotrophic plants
description: PPM_Analysis_Code_Dryad.R: R script used to process Illumina
 sequencing reads and perform all data formatting, statistical analyses,
 and figure generation.  PPM_bac.tre: Phylogenetic tree
 of all bacterial ASVs generated from the R package 'DADA2'. We
 used the software PASTA to generate the bacterial tree. 
 RDP_taxa.rds: R object that contains the taxonomy associated with
 each bacterial ASV generated from the R package 'DADA2'. We used
 the RDP classifer as implemented in DADA2 to assign taxonomy using the RDP
 training set 16.  sample_yields.csv: DNA concentration
 of the original DNA extractions and final amplicon libraries. 
 spe_table.rds: an ASV table which ennumerates the number of reads
 associated with each ASV in each sample. This data table was
 generated from the R package 'DADA2' and was used for all
 downstream analyses.
DOI: 10.5061/dryad.v6wwpzgqz
title: Data from: Resistance of soil biota and plant growth to disturbance increases with plant diversity

description: Plant diversity is critical to the functioning of ecosystems, potentially
 mediated in part by interactions with soil biota. Here, we characterized
 multiple groups of soil biota across a plant diversity gradient in a
 long-term experiment. We then subjected soil samples taken along this
 gradient to drought, freezing, and a mechanical disturbance to test how
 plant diversity affects the responses of soil biota and growth of a focal
 plant to these disturbances. High plant diversity resulted in soils that
 were dominated by fungi and associated soil biota, including increased
 arbuscular mycorrhizal fungi and reduced plant-feeding nematodes.
 Disturbance effects on the soil biota were reduced when plant diversity
 was high, resulting in higher growth of the focal plant in all but the
 frozen soils. These results highlight the importance of plant diversity
 for soil communities and their resistance to disturbance, with potential
 feedback effects on plant productivity.
DOI: 10.5061/dryad.q83bk3jdb
title: Data from: Carcass predictability but not domestic pet introduction affects functional response of scavenger assemblage in urbanised habitats

description: Urbanisation alters species richness and composition, but studies of
 urbanisation effects on ecological functions have often quantified
 variation in functional traits and changes in functional diversity rather
 than measuring directly how ecological functions vary between rural and
 urban assemblages. Consuming dead animal matter and recycling its
 nutrients stabilizes and structures food webs and therefore represents a
 key component of ecosystem functioning. Introduction of free-ranging
 domestic pet animals adds additional scavenger species to urban habitats,
 and increased predictability of carcass resources produced by human
 activities characterizes urban habitats. Here, we investigate the effect
 of urbanisation on the composition of diurnal and nocturnal scavenger
 assemblages and on the ecological function of carcass removal by using a
 carcass placement experiment in Swiss urban and adjacent rural habitats.
 While diurnal and nocturnal scavenger assemblages changed considerably
 from rural to urban areas by comprising particularly more domestic cats in
 the latter, carrion consumption rate did not differ between the two
 habitats. Predictability of carcass occurrence increased carrion
 consumption rate in both, urban and rural habitats but mainly native
 scavengers and not introduced domestic pets responded to the repeated
 placements. These results suggest that urbanisation shapes scavenger
 assemblage compositions without affecting their ecological function. The
 mechanism is likely due to a behavioural change of native scavengers in
 response to the occurrence of domestic pets resulting in functional
 plasticity of urban scavenger assemblages. The functional plasticity might
 be facilitated by the increased carcass predictability and additional
 anthropogenic food resources in urban habitats exploited by nutritionally
 flexible native scavenger species.
DOI: 10.5061/dryad.fn2z34tph
title: Data from: Parasite infection leads to widespread glucocorticoid hormone increases in vertebrate hosts: a meta-analysis

description: 1. Parasites and pathogens (hereafter parasites) commonly challenge
 organisms, but the extent to which their infections are physiologically
 stressful to hosts remains unclear. Importantly, vertebrate hormones,
 glucocorticoids (GCs), have been reported to increase, decrease, or show
 no alterations stemming from infections, challenging the generality of
 parasite-associated GC responses and motivating a search for important
 moderator variables. 2. We undertook the first meta-analysis of changes in
 vertebrate GCs following experimental infection with parasites, extracting
 146 effect sizes from 42 studies involving 32 host and 32 parasite species
 to test for general patterns of GC following infection, as well as the
 influence of moderators. 3. Overall, infection increased GCs relative to
 preliminary or control levels when the single largest effect sizes from
 repeated measures studies were examined, suggesting that parasites of
 vertebrate hosts can be thought of generally as physiological stressors by
 elevating GCs. 4. When all effect sizes were included along with the
 moderator of sampling time post-infection (tPI), parasite infection still
 had a positive effect on host GCs. However, the strength of that effect
 did not relate consistently to tPI, illustrating temporal differences in
 GC changes during the course of infection among parasite taxa (e.g.,
 arthropod versus bacterial infections). Other moderator variables examined
 did not influence GC responses. 5. Studies broadening the range of host
 and parasite taxa, and sampling during critical time windows, would aid in
 our understanding of variation in the host stress response and its
 consequences for fitness of both vertebrate hosts and their parasites.
 25-Sep-2019
DOI: 10.5061/dryad.12jm63xsr
title: Urbanization impacts apex predator gene flow but not genetic diversity across an urban-rural divide

description: Apex predators are important indicators of intact natural ecosystems. They
 are also sensitive to urbanization because they require broad home ranges
 and extensive contiguous habitat to support their prey base. Pumas (Puma
 concolor) can persist near human developed areas, but urbanization may be
 detrimental to their movement ecology, population structure, and genetic
 diversity. To investigate potential effects of urbanization in population
 connectivity of pumas, we performed a landscape genomics study of 130
 pumas on the rural Western Slope and more urbanized Front Range of
 Colorado, USA. Over 12,000 single nucleotide polymorphisms were genotyped
 using double-digest, restriction site-associated DNA sequencing
 (ddRADseq). We investigated patterns of gene flow and genetic diversity,
 and tested for correlations between key landscape variables and genetic
 distance to assess the effects of urbanization and other landscape factors
 on gene flow. Levels of genetic diversity were similar for the Western
 Slope and Front Range, but effective population sizes were smaller,
 genetic distances were higher, and there was more admixture in the more
 urbanized Front Range. Forest cover was strongly positively associated
 with puma gene flow on the Western Slope, while impervious surfaces
 restricted gene flow and more open, natural habitats enhanced gene flow on
 the Front Range. Landscape genomic analyses revealed differences in puma
 movement and gene flow patterns in rural versus urban settings. Our
 results highlight the utility of dense, genome-scale markers to document
 subtle impacts of urbanization on a wide-ranging carnivore living near a
 large urban center.
DOI: 10.5061/dryad.pnvx0k6h6
title: Within-host priority effects and epidemic timing determine outbreak severity in coinfected populations

description: Coinfections of hosts by multiple pathogen species are ubiquitous, but
 predicting their impact on disease remains challenging. Interactions
 between coinfecting pathogens within hosts can alter pathogen
 transmission, with the impact on transmission typically dependent on the
 relative arrival order of pathogens within hosts (within-host priority
 effects). However, it is unclear how these within-host priority effects
 influence multi-pathogen epidemics, particularly when the arrival order of
 pathogens at the host population scale varies. Here we combined models and
 experiments with zooplankton and their naturally co-occurring fungal and
 bacterial pathogens to examine how within-host priority effects influence
 multi-pathogen epidemics. Epidemiological models parameterized with
 within-host priority effects measured at the single host scale predicted
 that advancing the start date of bacterial epidemics relative to fungal
 epidemics would decrease mean bacterial prevalence in a multi-pathogen
 setting, while models without within-host priority effects predicted the
 opposite effect. We tested these predictions with experimental
 multi-pathogen epidemics. Empirical dynamics matched predictions from the
 model including within-host priority effects, providing evidence that
 within-host priority effects influenced epidemic dynamics. Overall,
 within-host priority effects may be a key element of predicting
 multi-pathogen epidemic dynamics in the future, particularly as shifting
 disease phenology alters the order of infection within hosts.
description: See Readme file for further instructions
DOI: 10.5061/dryad.zs7h44j4k
title: Eco-evolutionary significance of 'loners'

description: Loners, individuals out-of-sync with a coordinated majority, occur
 frequently in nature. Are loners incidental byproducts of large-scale
 coordination attempts or are they part of a mosaic of life-history
 strategies? Here, we provide empirical evidence of naturally occurring
 heritable variation in loner behavior in the model social
 amoeba Dictyostelium discoideum. We propose
 that Dictyostelium loners—cells that do not join the
 multicellular life-stage—arise from a dynamic population-partitioning
 process, the result of each cell making a stochastic, signal-based
 decision. We find evidence that this imperfectly synchronized
 multicellular development is affected by both abiotic (environmental
 porosity) and biotic (signaling) factors. Finally, we predict
 theoretically that when a pair of strains differing in their partitioning
 behavior co-aggregate, cross-signaling impacts slime-mold diversity across
 spatio-temporal scales. Our findings suggest that loners could be critical
 to understanding collective and social behaviors, multicellular
 development, and ecological dynamics in D. discoideum. More
 broadly, across taxa, imperfect coordination of collective behaviors might
 be adaptive by enabling diversification of life-history strategies.
description: Excel file containg the data used to create figures: 1, 3, 4,
 S1,  <b>Video S1:</b> Strain NC85.2 is
 shown aggregating in a 2% agar substrate.
 <b>Video S2:</b> Strain NC85.2 is shown aggregating
 in a 3% agar substrate. <b>Video S3:</b>
 Strain NC28.1 is shown aggregating in a 2% agar substrate.
 <b>Video S4:</b> Strain NC28.1 is shown aggregating
 in a 3% agar substrate. <b>Video S5:
 </b>Closeup of Video S2 in a region that ended up with high loner
 density. <b>Video S6:</b> Closeup of Video
 S2 in a region that ended up with low loner density.