cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s36hm11
title: Data from: Understanding the loss of maternal care in avian brood parasites using preoptic area transcriptome comparisons in brood parasitic and non-parasitic blackbirds

description: Parental care is critical for offspring survival in many species. However,
 parental behaviors have been lost in roughly 1% of avian species known as
 the obligate brood parasites. To shed light on molecular and
 neurobiological mechanisms mediating brood parasitic behavior, we compared
 brain gene expression patterns between two brood parasitic species and one
 closely related non-parasitic Icterid (blackbird) species. Our analyses
 focused on gene expression changes specifically in the preoptic area
 (POA), a brain region known to play a critical role in parental behavior
 across vertebrates. Using comparative transcriptomic approaches, we
 identified gene expression patterns associated with brood parasitism. We
 evaluated three non-mutually exclusive alternatives for the evolution of
 brood parasitism: (1) retention of juvenile-like (neotenic) gene
 expression, (2) reduced expression of maternal care-related genes in the
 POA, and/or (3) increased expression of genes inhibiting maternal care. We
 find evidence for neotenic expression patterns in both species of
 parasitic cowbirds as compared to maternal, non-parasites. In addition, we
 observed differential expression in a number of genes with previously
 established roles in mediating maternal care. Together, these results
 provide the first insight into transcriptomic and genetics mechanisms
 underlying the loss of maternal behavior in avian brood parasites.
description: bronze_annotated
 sequencesThe sequences generated
 from female bronzed cowbirds from Hildago county Texas with
 annotationsbronze_annotated.fastabrown_annotatedThe sequences generated from female brown-headed cowbirds from Hildago county Texas with annotationsred_annotatedThe sequences generated from female red-winged blackbirdsDE genes onlyResults of all possible pairwise comparisons
DOI: 10.5061/dryad.08vv722
title: Data from: Modeling multi-species and multi-mode contact networks: implications for persistence of bovine tuberculosis at the wildlife-livestock interface

description: 1. Individual- and species-level heterogeneity in contact rates can alter
 the ability of a pathogen to invade a host community. Many pathogens have
 multiple modes of transmission -- by direct or indirect contact. It is
 important to identify the role of heterogeneity in different types of
 transmission when managing the risk of disease spillover at the interface
 among different host species. 2. We developed a network-based analysis to
 explore how individual- and species-level heterogeneity shape multi-mode
 contact networks. We applied this network-based approach to contact data
 from proximity loggers collected in a multi-species host community that
 contributes to the spillover of the disease bovine tuberculosis (bTB) to
 cattle populations in Michigan, USA. We used this approach to quantify how
 individual- and species-level heterogeneity influence direct and indirect
 contacts in this system, explore how management interventions to control
 spillovers, such as the installation of deer fences, can alter observed
 contact networks and predict the role that wildlife species have in
 maintaining bTB in the community. 3. We found that individual- and
 species-level heterogeneity disproportionately influenced indirect and
 direct contact networks, with individual-level heterogeneity having a
 greater effect on indirect contact networks and species-level
 heterogeneity having a greater effect on direct contact networks. We also
 found that the installation of deer fences significantly reduced
 deer-specific indirect contacts. We used the results from our network
 analysis to show that white-tailed deer (Odocoileus virginianus) could act
 as the sole reservoir host for bTB in this community with important
 implications for understanding past bTB dynamics and managing the
 persistence of bTB in the future. 4. Synthesis and applications: Analyses
 of epidemiological networks rarely account for multiple modes of contact,
 which can lead to an incomplete understanding of how individual- and
 species-level heterogeneity affect disease transmission. The multi-mode,
 multi-species network analysis we develop in this study, illustrates that
 individual- and species-level heterogeneity can play significantly
 different roles depending on the type of contact network considered. This
 has important implications when managing disease at the wildlife-livestock
 interface, where strategies may need to be multi-pronged to account for
 the variable role of heterogeneity on different modes of
 contact.11-Feb-2019
description: Contact data used to
 analyze multi-species, multi-mode contact networksThe zip file contains
 the data and corresponding metadata for the for the contact analyses used
 in the corresponding publication.contact_data.zip
DOI: 10.5061/dryad.mr479dj
title: Data from: Competitive responses of eight old-field plant species in four environments

description: Variation in relative competitive abilities among environments has been
 proposed to control the species composition of plant communities. We
 tested whether the competitive responses of eight species varied with
 fertility and disturbance in an old field. We also tested whether the
 competitive effects of vegetation varied with fertility and disturbance in
 an old field. We also tested whether the competitive effects of vegetation
 varied with fertility and disturbance. Plots received one of four
 combinations of nitrogen (added or not) and disturbance (tilled or not) in
 each of five years. There were 10 replicates of each treatment. In the
 fifth summer, transplants of eight species comprising annual and perennial
 forbs and grasses were grown in all four combinations of the N and
 disturbance treatments. Transplants were grown in subplots with all
 neighbors, with only roots of neighbors, or with no neighbors. Transplant
 roots and shoots were harvested after one summer and individual growth
 rates were determined. Growth rate varied significantly with the
 interaction among species, competition, and N, suggesting that species
 differed in their competitive responses and that these differences varied
 with N availability. Comparisons among competition treatments at each
 level of N showed six distinct responses in the eight species examined.
 The competitive effect of neighboring vegetation shifted from roots to
 shoots as N increased, but decreased in disturbed plots. The total effect
 of competition increased significantly with neighbor mass in 4 of the 32
 examined (eight species in four combinations of N and disturbance). All
 four cases involved annuals in annual neighborhoods. The results for eight
 species confirmed earlier single—species diverged in their responses to
 competition as soil N availability varied.
description: WilsonTilman95TargetsTarget masses in four environments and three competition treatments.WilsonTilman95NbrsNeighbour masses, shoots and roots.
DOI: 10.5061/dryad.8476811
title: Data from: Crowded developmental environment promotes adult sex-specific nutrient consumption in a polyphagous fly

description: Background: The fitness of holometabolous insects depends largely on
 resources acquired at the larval stage. Larval density is an important
 factor modulating larval resource-acquisition, influencing adult survival,
 reproduction, and population maintenance. To date, however, our
 understanding of how larval crowding affects adult physiology and
 behaviour is limited, and little is known about how larval crowding
 affects adult non-reproductive ecological traits. Here, larval density in
 the rearing environment of the polyphagous fruit fly Bactrocera tryoni
 (‘Queensland fruit-fly’) was manipulated to generate crowded and uncrowded
 larval treatments. The effects of larval crowding on pupal weight, adult
 emergence, adult body weight, energetic reserves, fecundity, feeding
 patterns, flight ability, as well as adult predation risk were
 investigated. Results: Adults from the crowded larval treatment had lower
 adult emergence, body weight, energetic reserves, flight ability and
 fecundity compared to adults from the uncrowded larval treatment. Adults
 from the crowded larval treatment had greater total food consumption
 (i.e., consumption of yeast plus sucrose) relative to body weight for both
 sexes compared to adults from the uncrowded treatment. Furthermore, males
 from the crowded treatment consumed more yeast relative to their body
 weight than males from the uncrowded treatment, while females from the
 crowded treatment consumed more sucrose relative to their body weight than
 females from the uncrowded treatment. Importantly, an interaction between
 the relative consumptions of sucrose and yeast and sex revealed that the
 density of conspecifics in the developmental environment differentially
 affects feeding of adult males and females. We found no effect of larval
 treatment on adult predation probability. However, males were
 significantly more likely to be captured by ants than females. Conclusion:
 We show that larvae crowding can have important implications to ecological
 traits in a polyphagous fly, including traits such as adult energetic
 reserve, flight ability, and adult sex-specific nutrient intake. Our
 findings contextualise the effects of larval developmental conditions into
 a broad ecological framework, hence providing a better understanding of
 their significance to adult behaviour and fitness. Furthermore, the
 knowledge presented here can help us better understanding downstream
 density-dependent effects of mass rearing conditions of this species, with
 potential relevance to Sterile Insect Technique.
description: Morimotoetal-FrontInZoology-2019The file contains the raw data for all analyses performed in the Morimoto et al 2019 Front in Zool paper. Different datasets are provided as tabs.
DOI: 10.5061/dryad.455mv2m
title: Data from: Impacts of salt stress on locomotor and transcriptomic responses in the intertidal gastropod Batillaria attramentaria

description: Salinity is one of the most crucial environmental factors that structures
 biogeographic boundaries of aquatic organisms, affecting distribution,
 abundance, and behavior. However, the association between behavior and
 gene regulation underlying acclimation to changes in salinity remains
 poorly understood. In this study, we investigated the effects of salinity
 stress on behavior (movement distance) and patterns of gene expression
 (using RNA-seq) of the intertidal gastropod Batillaria attramentaria. We
 examined responses to short- (1 hour) and long-term (30 day) acclimation
 to a range of salinities (43, 33 (control), 23, 13, and 3 Practical
 Salinity Units (PSU)). We found that the intertidal B. attramentaria is
 able to tolerate a broad range of salinity from 13 to 43 PSU, but not the
 acute low salinity of 3 PSU. Behavioral experiments showed that salt
 stress significantly influenced snails’ movement, with lower salinity
 resulting in shorter movement distance. Transcriptomic analyses revealed
 critical metabolic pathways and genes potentially involved in acclimation
 to salinity stress, including ionic and osmotic regulation, signal and
 hormonal transduction pathways, water exchange, cell protection, and gene
 regulation or epigenetic modification. In general, our study presents a
 robust, integrative laboratory-based approach to investigate the effects
 of salt stress on a non-model gastropod, which is facing detrimental
 consequences of environmental change. The current genetic results provide
 a wealth of reference data for further research on mechanisms of ionic and
 osmotic regulation and adaptive evolution of this coastal gastropod.
description: Locomotor and
 transcriptional responses of B. attramentaria to salt
 stress"Footage
 videos" compressed file contains 60 sub-folders named by day recorded
 and exposure salinity. For example, videos in Day 1 (16.09.07)_13PSU
 folder were generated in Day 1 (date recorded September 7th, 2016) by
 recording snails exposed to 13 PSU saline water. This compressed file was
 generated using Winzip version 23. The other 12 compressed files are
 assembly BAM files of RNAseq data obtained from 12 individuals acclimated
 to different salinity conditions (13, 23, 33, and 43 PSU) with 3 replicate
 per salinity condition.Footage
 Videos.zipKorea_Tsushima_Hajeonri_13PSU-1Korea_Tsushima_Hajeonri_13PSU-2Korea_Tsushima_Hajeonri_13PSU-3Korea_Tsushima_Hajeonri_23PSU-1Korea_Tsushima_Hajeonri_23PSU-2Korea_Tsushima_Hajeonri_23PSU-3Korea_Tsushima_Hajeonri_33PSU-1Korea_Tsushima_Hajeonri_33PSU-2Korea_Tsushima_Hajeonri_33PSU-3Korea_Tsushima_Hajeonri_43PSU-1Korea_Tsushima_Hajeonri_43PSU-2Korea_Tsushima_Hajeonri_43PSU-3
DOI: 10.5061/dryad.5t9211b
title: Data from: Evolution of stress-induced mutagenesis in the presence of horizontal gene transfer

description: Stress-induced mutagenesis has been observed in multiple species of
 bacteria and yeast. It has been suggested that in asexual populations, a
 mutator allele that increases the mutation rate during stress can sweep to
 fixation with the beneficial mutations it generates. However, even asexual
 microbes can undergo horizontal gene transfer and rare recombination,
 which typically interfere with the spread of mutator alleles. Here we
 examine the effect of horizontal gene transfer on the evolutionary
 advantage of stress-induced mutator alleles. Our results demonstrate that
 stress-induced mutator alleles are favored by selection even in the
 presence of horizontal gene transfer, and more so when the mutator alleles
 also increase the horizontal gene transfer rate. We suggest that when
 regulated by stress, mutation and horizontal gene transfer can be
 complementary, rather than competing, adaptive strategies, and that
 stress-induced mutagenesis has important implications for evolutionary
 biology, ecology, and epidemiology, even in the presence of horizontal
 gene transfer and rare recombination.
description: Simulation and analysis
 dataIncludes results of
 invasion and adaptation simulations, and of stability
 analysis.dryad.zip
DOI: 10.5061/dryad.nh3ss87
title: Data from: Experimental increase in temperature affects eggshell thickness, and not egg mass, eggshell spottiness or egg composition in the great tit (Parus major)

description: Phenotypic effects of global warming have been documented in many
 different taxa. However, the importance of transgenerational phenotypic
 plasticity in these adaptations are seldom studied. In birds, temperature
 could affect egg characteristics. Higher temperatures during egg-laying
 may reduce maintenance costs for females and allow a higher investment in
 reproduction. Yet, females may also use temperatures as a cue for the risk
 of mismatch latter in the season. Thus, higher temperatures may be
 correlated to an acceleration of embryonic development (e.g. via hormonal
 manipulation). We performed an experiment in which night-time temperature
 was increased in the nestbox by approximately 1°C throughout the entire
 laying period in great tits (Parus major). We collected one pre-treatment
 egg (beginning of the laying sequence) and one post-treatment egg (end of
 the laying sequence). Egg content (yolk androgens and lysozymes in the
 albumen), eggshell coloration, eggshell mass, egg mass, and shape were not
 affected by the treatment. However, last-laid eggs in clutches from
 control nestboxes had a thicker eggshell than last-laid eggs from heated
 nestboxes, suggesting a putative slight decrease of maternal investment
 with the experimental increase of temperature. We also observed effects of
 the laying sequence on egg characteristics. Eggs that were laid late in
 the laying sequence were heavier, larger, had larger spots and higher yolk
 androgens than eggs laid earlier. Lysozyme concentration decrease with the
 laying sequence in late clutches only. Thus, effects of temperature may
 also change with the laying sequence and it would be interesting in the
 future to tests the effects on first-laid eggs.
description: data-nestboxdata-egg-characteristicdata-eggshell-picturesdata-androgensdata-testo.csvdata-lysozymes
DOI: 10.5061/dryad.873r5r3
title: Data from: Predicting the impacts of climate change on Papio baboon biogeography: are widespread, generalist primates ‘safe’?

description: Aims: To explore whether wide-ranging, generalist primates like baboons
 can be presumed ‘resilient’ in the face of climate change. We identify
 environmental variables influencing baboons’ current distributions and
 predict their future potential distributions under different climate
 change scenarios. Location: Africa and Arabia. Taxon: Baboons, Papio spp.
 Methods: We used localities for olive, yellow, Guinea, hamadryas, chacma
 and Kinda baboons together with high-resolution data on bioclimatic
 variables, altitude and vegetation to construct species distribution
 models (SDMs). These SDMs were run under current and future conditions,
 with future models based on three General Circulation Models (MIROC-ESM,
 CCSM4 and HadGEM2-ES) under two Representative Concentration Pathways
 (RCP2.5 and 6.0) for 2050 and 2070 to explore a range of different
 possible futures. Results: All SDMs produced AUC values &gt;0.916
 suggesting excellent overall performance. Altitude was the most important
 variable influencing Guinea baboon distributions (contributing 41.6%),
 temperature seasonality for olive and yellow baboons (47.5% and 35.4%
 respectively), precipitation of the driest month for hamadryas baboons
 (24.4%), annual mean precipitation for the Kinda baboon (45.1%) and mean
 temperature of the driest quarter for chacma baboons (41.4%). Chacma and
 Kinda baboons are predicted to suffer substantial habitat loss, and Guinea
 baboons may do the same if conditions aridify as climates warm. In
 contrast, all models for the olive and hamadryas baboons predicted an
 increase in suitable habitat and only smaller changes were predicted for
 the yellow baboon. Main conclusions: Two or three of six baboon taxa are
 at risk of significant habitat loss as climates warm despite their
 apparent ecological flexibility. The chacma and Kinda baboons (both IUCN
 listed as Least Concern) will be worst affected, followed by the Guinea
 baboon (Near Threatened) if warming brings aridification. We recommend
 more focus on biogeographic tools as a means of exploring vulnerabilities
 in seemingly resilient species.
description: Hill&Winder-Baboon-biogeography-data-depositThis file contains locality samples and model outputs, including average grids for current niche models. There is a ReadMe text file included explaining the naming, and the accompanying paper gives details of the environmental layer sources too. Further details and additional maps/grids are available on request from i.c.winder@bangor.ac.uk.
DOI: 10.5061/dryad.631j930
title: Data from: Effects of vertical position on trematode parasitism in larval anurans

description: Spatial distributions of animals can affect interactions with their
 natural enemies, such as parasites, and thus have important implications
 for host-parasite dynamics. While spatial variation in infection risk has
 been explored in many systems at the landscape scale, less attention has
 been paid to spatial structure at smaller scales. Here, we explore a
 hypothesized relationship between a common spatial variable, vertical
 position, and risk of parasite infection in a model aquatic system, larval
 frogs (Rana) and trematode (Digenea) parasites. Vertical position is
 relevant to this system given evidence that the densities of snail first
 intermediate hosts, larval frogs second intermediate hosts, and trematode
 infective stages can vary with depth. To test the effects of depth on
 infection risk of larval frogs by trematodes, we performed two enclosure
 experiments, one in the laboratory and one in the field, in which larval
 frogs in cages just below the water surface or near the bottom of the
 water column were exposed to parasites. Compared to near-surface cages,
 mean infection load (number of cysts) in tadpoles in near-bottom cages was
 83% higher after 48-hour exposures in the laboratory and 730% higher after
 10-day exposures in the field. Our findings thus indicate that infection
 risk depends on depth, which may have adaptive significance, as tadpoles
 have previously been shown to change vertical position in response to
 parasite presence. These results motivate future work examining vertical
 variation in infection risk and may have broader implications for
 host-parasite dynamics and evolution of host and parasite behavior.
description: Lab Experiment Infection
 Load DataData on echinostome
 infection load in tadpoles in three groups (near surface, near bottom, or
 free) in laboratory experiment.Lab_Experiment_Infection_Load.xlsxField Experiment Infection Load and SVL dataFinal infection load (intrarenal and extrarenal cysts) in tadpoles from near-surface or near-bottom enclosures in a field experiment in a pond in Illinois.Field_Experiment_Infection_Load_SVL.xlsxField Experiment Survival and Prevalence DataData for survival of tadpoles and prevalence (proportion of tadpoles infected with intrarenal and extrarenal trematode cysts).Field_Experiment_Survival_Prevalence.xlsx
DOI: 10.5061/dryad.c58539p
title: Data from: The population genetic diversity and pattern of Pteroceltis tatarinowii, a relic tree endemic to China, inferred from SSR markers

description: Pteroceltis tatarinowii, a relic tree endemic to China, is mainly
 distributed in limestone mountains and has a wide geographical range. In
 this study, 12 microsatellite primer pairs were assayed to analyse the
 genetic pattern and gene flow among 461 individuals sampled from 23 wild
 populations of P. tatarinowii. A high level of genetic diversity was
 detected based on high values of total alleles (159), the number of
 alleles (NA = 6.373), expected heterozygosity (HE = 0.696) and observed
 heterozygosity (HO = 0.679). The high genetic diversity in this species
 was attributed to its long-life history, large-scale geographical
 distribution and wind dispersal breeding system. Low genetic
 differentiation (GST = 0.137, FST = 0.138) was found among the populations
 of P. tatarinowii. The genetic variation occurred mostly within the
 populations. Gene flow was estimated to be 1.562. This moderate level of
 gene flow could decrease interpopulation differentiation by buffering
 against genetic drift and improving gene exchange. The spatial genetic
 structure of P. tatarinowii occurred at the whole-region scale (r = 0.311,
 P &lt; 0.05) and in the region of South China (r = 0.453, P &lt;
 0.05), which might be related to terrain heterogeneity and the demographic
 history of P. tatarinowii. The distinct east-west high mountains
 distributed in South China might serve as physical barriers to seed and
 pollen flow. The isolation and local adaptation of different refugia could
 further limit normal gene flow. In addition, far-apart populations might
 fail to effectively disperse pollen and seeds. Based on the
 above-mentioned results, some tentative suggestions for protection are
 presented for this species.
description: Compressed raw data
 setThe uploaded data file
 includes the raw data for the figures and tables in our
 paper.raw
 data.zip