cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fd713fs
title: Data from: Elevated temperatures translate into reduced dispersal abilities in a natural population of an aquatic insect

description: 1. Rising global temperatures force many species to shift their
 distribution ranges. However, whether or not (and how fast) such range
 shifts occur depends on species’ dispersal capacities. In most ecological
 studies, dispersal-related traits (such as the wing size or wing loading
 in insects) are treated as fixed, species-specific characteristics,
 ignoring the important role of phenotypic plasticity during insect
 development. 2. We tested the hypothesis that dispersal-related traits
 themselves vary in dependence of ambient environmental conditions
 (temperature regimes, discharge patterns and biotic interactions during
 individual development). 3. We collected data over 8 years from a natural
 population of the crane fly Tipula maxima in central Germany. Using linear
 mixed-effect models, we analysed how phenotypic traits, phenological
 characteristics and population densities are affected by environmental
 conditions during the preceding 3, 6 and 12 months. 4. We found a moderate
 (5.6%) increase in wing length per 1°C increase of mean annual
 temperatures during the previous year. At the same time, body weight
 increased by as much as 17.8% in females and 26.9% in males per 1°C,
 likely driven by increased habitat productivity, which resulted in a 16.4%
 (female) and 19.3% (male) increased wing loading. We further found a
 shorter, more synchronized emergence period (i.e., a narrower time frame
 for dispersal) with increasing temperatures. 5. Altogether, our results
 suggest that dispersal abilities of T. maxima were negatively affected by
 elevated temperatures, and we discuss how similar patterns might affect
 the persistence of populations of other aquatic insects, especially
 stenoecious taxa with narrow distribution ranges. Our study calls for
 integration of information on temperature-induced phenotypic plasticity of
 dispersal-related traits into models forecasting range shifts in the face
 of climate change. Furthermore, the patterns reported here are likely to
 affect metapopulation dynamics of aquatic insects under climate change
 conditions and may contribute to the ongoing decline of insect biomass and
 diversity.
description: Data from: Elevated
 temperatures translate into reduced dispersal abilities in a natural
 population of an aquatic insectData on emergence of
 Tipula maxima, with individual wing length, body weight and wing loading.
 Additional information on water temperature, mean and maximum discharge
 during development.Jourdan et al Tipula Dryad
 JAE-2019-00249.csv
DOI: 10.5061/dryad.qt8mr4v
title: Data from: Urban bumblebees are smaller and more phenotypically diverse than their rural counterparts

description: 1. With urbanization identified as being one of the key drivers of change
 in global land use, and the rapid expansion of urban areas worldwide, it
 is relevant to evaluate how novel ecological conditions in cities shape
 species functional traits, which are essential for how species interact
 with their environments and with each other. 2. Despite the many
 comparative studies on organisms living in urban and non-urban areas our
 knowledge on species responses to urban environments remains limited. For
 one, much of the ecological research has assumed that the environment
 changes in a linear fashion from the city core to the city edges, whereas
 in reality the environments within the cities are highly heterogeneous.
 Furthermore, studies on species responses to these highly variable
 ecosystems are often based on interspecific mean trait values, which
 ignore the potential for high levels of intraspecific variation among
 individuals in key functional traits. 3. The current study investigated
 intraspecific functional trait differences for four functional traits
 associated with body size, mobility, and resource selection among rural
 and urban populations of two common bumblebee species, Bombus pascuorum
 and Bombus lapidarius, in urban centers and adjacent rural areas in
 Switzerland. 4. We document shifts in functional traits towards smaller
 individuals and higher multidimensional trait variation in urban
 populations compared to rural conspecifics of both species. This shows
 that urban individuals for both species are on average smaller sized but
 populations are distinctively different from rural population by
 increasing their trait richness and diversifying their trait combinations.
 In addition, we found bimodality in tongue length within urban B.
 pascuorum populations. 5. Our results suggest that urban and rural
 populations possibly experience differential selection pressures resulting
 in trait differences across and among populations. We argue that
 variations in the respective foraging landscapes in cities leads to
 smaller-sized but phenotypically more diverse populations, and drive
 functional trait divergence.
description: Bumblebee_Data_Eggenberger_et.al_JAE_2019Data file containing the individual trait measurements of the two bumblebee species, B. lapidarius and B. pascuorum, from urban and rural habitats in Switzerland
DOI: 10.5061/dryad.qv9471s
title: Data from: Species composition and community structure of small pest rodents (Muridae) in cultivated and fallow fields in maize growing areas in Mayuge district, Eastern Uganda

description: 1. Pest rodents remain key biotic constraints to cereal crops production
 in the East African region where they occur, especially in seasons of
 outbreaks. Despite that, Uganda has scant information on rodents as crop
 pests to guide effective management strategies. 2. A
 Capture-Mark-Recapture (CMR) technique was employed to establish the
 species composition and community structure of small rodents in a
 maize-based agro ecosystem. Trapping of small rodents was conducted in
 permanent fallow and cultivated fields, each category replicated twice
 making four grids. At each field, a 6060 m grid was measured and marked
 with permanent trapping points spaced at 1010 m, making a total of 49
 trapping points/grids. Trapping was conducted monthly at 4 weeks interval
 for three consecutive days for two and half years using Sherman Live
 traps. 3. Eleven identified small rodent species and one insectivorous
 small mammal were recorded with Mastomys natalensis being the most
 dominant species (over 60.7%). Other species were Mus triton (16.1%),
 Aethomys hendei (6.7%), Lemniscomys zebra (5.2%), Lophuromys sikapusi
 (4.8%), Arvicanthis niloticus (0.9%), Gerbilliscus kempi (0.1%),
 Graphiurus murinus (0.1%), Steatomys parvus (0.1%), Dasymys incomtus
 (0.1%) and Grammomys dolichurus (0.1%). Spatially, species richness
 differed significantly (p = 0.0001) between the studied field habitats
 with significantly higher richness in fallow land compared to cultivated
 fields. 4. Temporally, total species richness and abundance showed a
 significant interaction effect over the months, years and fields of
 trapping with significantly (p = 0.001) higher abundances during months of
 wet seasons and in the first and third year of trapping. In terms of
 community structure, higher species diversity associated more with fallow
 field habitats but also with certain rare species found only in cultivated
 fields. 5. Synthesis and applications. Currently, management strategies
 can be designed to target the key pest species and the most vulnerable
 habitats.
description: Data from: Species
 Composition and Community Structure of Small Pest Rodents (Muridae) in
 Cultivated and Fallow Fields in Maize Growing Areas in Mayuge district,
 Eastern UgandaData was collected from
 Capture Mark Release experiment that were set in cultivated and fallow
 filed habitats in Mayuge district, eastern Uganda. the CMR was ru for 2
 years from 2016-2018. data was collected on a monthly basis from all the 4
 field habitatsspecies_composition_and_community_structure_Mayuge_Uganda.csv
DOI: 10.5061/dryad.2nv32qh
title: Data from: Drivers and patterns of microbial community assembly in a Lyme disease vector

description: Vector-borne diseases constitute a major global health burden and are
 increasing in geographic range and prevalence. Mounting evidence has
 demonstrated that the vector microbiome can impact pathogen dynamics,
 making the microbiome a focal point in vector-borne disease ecology.
 However, efforts to generalize preliminary findings across studies and
 systems and translate these findings into disease control strategies are
 hindered by a lack of fundamental understanding of the processes shaping
 the vector microbiome and the interactions therein. Here we use 16S rRNA
 sequencing and apply a community ecology framework to analyze microbiome
 community assembly and interactions in Ixodes pacificus, the Lyme disease
 vector in the western US. We find that vertical and environmental
 transmission routes drive population-level patterns in I. pacificus
 microbial diversity and composition, but not in microbial function and
 overall abundance. Further we find that the I. pacificus microbiome is not
 strongly structured based on competition but assembles non-randomly,
 likely due to vector-specific filtering processes which largely eliminate
 all but the dominant endosymbiont, Rickettsia. At the scale of the
 individual I. pacificus, we find support for a highly limited internal
 microbial community, and propose that the tick endosymbiont may be the
 most important component of the vector microbiome in influencing pathogen
 dynamics.
description: OTU
 tableThis table list
 percentage relative abundance for each OTU retained after the sequence
 quality filtering pipeline for each sample included in this study. The
 treatment group (both clutch and environmental exposure time) is also
 listed for each sample.MicrobialCommunityAssembly_Dryad.csv
DOI: 10.5061/dryad.3jt83k4
title: Data from: Evolution of the intermuscular bones in the Cyprinidae (Pisces) from a phylogenetic perspective

description: Intermuscular bones (IBs) are widely present in morphologically
 generalized teleost fishes, and are commonly found in the Cyprinidae. IBs
 are small, hard spicules of bone that form by ossification in the myosepta
 between neighboring myomeres. Why fish have IBs, and whether there is any
 evolutionary pattern to their occurrence, have been poorly understood.
 However, the presence of IBs do substantially affect the meat quality and
 commercial values of many cyprinid fishes in aquaculture. In this study,
 we sampled 592 individuals of cyprinid fishes to systematically
 investigate the evolution of IBs from a phylogenetic point of view. We
 found that the total number of IBs in the Cyprinidae ranged from 73 to
 169, and we clarified that only two categories of IBs (epineural and
 epipleural) were present in all examined cyprinids. Most of the IBs were
 distributed in the posterior region of the fish, which might be an optimal
 target for selecting fewer IBs strains in aquaculture. There was a
 positive correlation between IBs and the number of vertebrae, thus making
 it possible to predict the approximate number of IBs by counting the
 number of vertebrae. Although the IBs displayed some correlation with
 phylogenetic relationships in some lineages and to ecological factors such
 as diet (especially carnivore), in an overall view the variations of IBs
 in cyprinids were extremely diverse. The number and patterns of IBs in
 these fishes may reflect their phylogenetic history, but has been shaped
 by multiple environment factors. In this study, we also confirmed that
 X-ray photography remains an optimal and reliable method for the study of
 IBs.
description: Dataset
 S1DNA
 sequence alignment for the concatenated dataset with three genes in nexus
 format.Dataset
 S2Input file for Bayesian
 inference (BI) analyses of the concatenated dataset in nexus
 format.Dataset
 S3Input file for Mesquite
 analysis in nexus format.
DOI: 10.5061/dryad.64d2h47
title: Data from: Geographic variation in dispersal distance facilitates range expansion of a lake shore plant in response to climate change

description: Aim: Geographic variation in dispersal abilities is widespread and likely
 to affect species’ range dynamics in response to climate change. However,
 distribution models that predict climate-induced range shifts do not
 account for spatial variation in dispersal. We developed an eco-genetic
 model to investigate how variation in dispersal distances across a
 species’ range could interact with climate-induced selection and alter
 predicted range dynamics in a species with documented variation in
 dispersal traits. Location: We investigated the range of an annual plant,
 Cakile edentula var. lacustris, which occupies beaches spanning a 555 km
 latitudinal gradient along the Laurentian Great Lakes. Methods: We built a
 hybrid model that combines climatic niche modeling, based on decadal
 climate projections, with an individual-based model that allows for
 evolutionary processes to act upon a heritable dispersal kernel. We
 evaluated how spatial variation in dispersal distance and dispersal
 evolution influenced range dynamics, spatial and temporal variation in
 dispersal, and the distribution of neutral genetic variation. The model
 was parametrized with data on C. edentula’s distribution, life history,
 and dispersal characteristics. Results: Geographic variation in dispersal
 distance, adaptive dispersal evolution, and dispersal distance increased
 the potential for local populations of C. edentula to keep pace with
 changing climatic conditions through range shifts. Dispersal distances
 always increased at the expanding and contracting range edges when
 dispersal was allowed to evolve. Furthermore, scenarios where dispersal
 distances were initially lower at the range edges resulted in the largest
 evolutionary changes over 105 years (&gt; 1.5 km increase in mean
 distance at northern edge). Adaptive dispersal evolution always reduced
 neutral genetic diversity across the species’ range. Main conclusions:
 Variation in dispersal abilities across C. edentula’s range and adaptive
 evolution led to different predicted outcomes in range dynamics during
 climate change illustrating the importance of including spatial variation
 in dispersal into species distribution models.
description: Code for dispersal
 individual-based modelThe zipped folder
 contains the climate suitability maps and all R code to run the hybrid
 individual-based model for the article published in Diversity and
 Distributions "Geographic variation in dispersal and dispersal
 distance facilitate range expansion of a lakeshore plant in response to
 climate change".model.code.zip
DOI: 10.5061/dryad.g11gs40
title: Data from: Size-abundance rules? evolution changes scaling relationships between size, metabolism and demography

description: Body size often strongly covaries with demography across species.
 Metabolism has long been invoked as the driver of these patterns but tests
 of causal links between size, metabolism and demography within a species
 are exceedingly rare. We used 400 generations of artificial selection to
 evolve a 2427% size difference in the microalga Dunaliella tertiolecta. We
 repeatedly measured size, energy fluxes and demography across the evolved
 lineages. Then, we used standard metabolic theory to generate predictions
 of how size and demography should covary based on the scaling of energy
 fluxes that we measured. The size-dependency of energy remained relatively
 consistent in time, but metabolic theory failed to predict demographic
 rates, which varied unpredictably in strength and even sign across
 generations. Classic theory holds that size affects demography via
 metabolism – our results suggest that both metabolism and size act
 separately to drive demography and that among-species patterns may not
 predict within-species processes.
description: All data and R
 codesInstructions - “Scaling
 coef (Fig2-4)” This main file is called “Final analysis.R” and will
 produce figure 2 to 4 and all tables in the supplementary materials. Open
 it with statistical software R. Within the script file: (1) check that all
 packages are installed in the computer (otherwise install before running
 the script), and (2) set the directory where the script (.R) file is in
 the computer. After having done that, everything else should work by
 running the file in R. The script will read all data, all functions (in
 the script “Functions.R”), calculate and save the tables (in folder
 “Tables”), and plot and save the images (in folder “Figures”). “Size
 trajectories (Fig1)” This file will create figure 1. It will read the raw
 data, calculate running means for each treatment, and plot the figures.
 Points represent each replicate culture, and lines represent each running
 mean. All files were created using R version 3.5.1 (2018-07-02) and were
 designed to run in Mac computers.All
 data.zip
DOI: 10.5061/dryad.27jp751
title: Data from: Phylogeography and paleodistribution models of a widespread birch (Betula platyphylla Suk.) across East Asia: multiple refugia, multidirectional expansion, and heterogeneous genetic pattern

description: Widespread tree species cover large geographical areas and play important
 roles in various vegetation types. Understanding how these species
 responded to historical climatic changes is important for understanding
 community assembly mechanisms with evolutionary and conservation
 implications. However, the location of refugial areas and postglacial
 history of widespread trees in East Asia remain poorly known. We combined
 microsatellite data (63 populations, 1756 individuals) and ecological
 niche modeling to examine the range-wide population diversity, genetic
 structure and historical demography of a pioneer tree species, Asian white
 birch (Betula platyphylla Suk.) across East Asia. We found a north to
 south trend of declining genetic diversity and five clusters,
 corresponding to geographic regions. Different clusters were inferred to
 have diverged through Pleistocene climatic oscillations and have different
 expansion routes, leading to genetic admixture in some populations.
 Ecological niche models indicated that the distribution of Betula
 platyphylla during the Last Glacial Maximum still had a large latitude
 span with slight shifts towards southeast, and northern populations had
 more variable distribution ranges than those in the south during later
 climatic oscillations. Our results reflect the relatively stable
 distribution through the last glacial-interglacial cycles and recent
 multidirectional expansion of Betula platyphylla, providing new hypotheses
 for the response pattern of widespread tree species to climate change. The
 gradual genetic pattern from northeast to southwest and alternative
 distribution dynamics possibly resulted from environmental differences
 caused by latitude and topographic heterogeneity.
description: Genotype
 filesnSSR genotype
 files
DOI: 10.5061/dryad.hb3f25t
title: Data from: Feeding in murky waters: acclimatization and landmarks improve foraging efficiency of zebrafish (Danio rerio) in turbid waters

description: Fish inhabiting human-dominated ecosystems are prone to altered sensory
 environments in which they must live and function. Increased turbidity is
 one such change that they must deal with. We tested whether an increase in
 water turbidity and presence of visual landmarks (coloured stones) affect
 the foraging efficiency of wild zebrafish. We also tested the influence of
 extended exposure to differing turbidity levels on the subsequent foraging
 efficiency of acclimatized individuals. Feeding latency (time taken to
 find food) increased significantly with increase in turbidity levels from
 a minimum of 4 s to ca. 300 s. However, extended exposure of fish to
 varying levels of turbidity decreased feeding latencies in acclimatized
 conditions, indicating that acclimatization to the immediate visual
 environment plays an important role in determining foraging success. Most
 significantly, we found that feeding latencies in turbid conditions
 decreased significantly if visual landmarks were present. This
 demonstrates that zebrafish utilize visual landmark cues to navigate to
 foraging sites when visibility is impaired. This study has important
 implications on the role of behavioural plasticity and spatial learning in
 animals that allow them to cope with altered sensory environments such as
 episodes of enhanced turbidity that could be natural or anthropogenic.
description: BL_Rawdata_SekharetalRaw data on feeding latency of zebrafish to examine foraging efficiency in water with varying turbidity. File also contains data on foraging efficiency in presence and absence of visual landmarks.
DOI: 10.5061/dryad.vb658bc
title: Data from: The environmental and genetic determinants of chick telomere length in Tree Swallows ( Tachycineta bicolor )

description: Conditions during early life can have dramatic effects on adult
 characteristics and fitness. However, we still know little about the
 mechanisms that mediate these relationships. Telomere shortening is one
 possibility. Telomeres are long sequences of DNA that protect the ends of
 chromosomes. They shorten naturally throughout an individual’s life, and
 individuals with short telomeres tend to have poorer health and reduced
 survival. Given this connection between telomere length (TL) and fitness,
 natural selection should favor individuals that are able to retain longer
 telomeres for a greater portion of their lives. However, the ability of
 natural selection to act on TL depends on the extent to which genetic and
 environmental factors influence TL. In this study, we experimentally
 enlarged broods of Tree Swallows (Tachycineta bicolor) to test the effects
 of demanding early-life conditions on TL, while simultaneously
 cross-fostering chicks to estimate heritable genetic influences on TL. In
 addition, we estimated the effects of parental age and chick sex on chick
 TL. We found that TL is highly heritable in Tree Swallow chicks, and that
 the maternal genetic basis for TL is stronger than is the paternal genetic
 basis. In contrast, the experimental manipulation of brood size had only a
 weak effect on chick TL, suggesting that the role of environmental factors
 in influencing TL early in life is limited. There was no effect of chick
 sex or parental age on chick TL. While these results are consistent with
 those reported in some studies, they are in conflict with others. These
 disparate conclusions might be attributable to the inherent complexity of
 telomere dynamics playing out differently in different populations or to
 study-specific variation in the age at which subjects were measured.
description: Belmaker et al 2019.
 Ecology and Evolution
DOI: 10.48596/pgn.rnvh3p1-8.richmondca.p52s1
title: Pandora 52s1 sky NO2 surface number density, partial and tropospheric column amount at RichmondCA; Processing Code: nvh3; Processor Version: 1-8
DOI: 10.48596/pgn.rfuh5p1-8.richmondca.p52s1
title: Pandora 52s1 sky H2CO surface number density, partial and tropospheric column amount at RichmondCA; Processing Code: fuh5; Processor Version: 1-8