cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rn8pk0pbm
title: Trachemys scripta gene expression data under constant and fluctuating incubation temperatures

description: There is ample research demonstrating that temperature can have complex
 effects on biological processes, including the timing of when organisms
 respond to temperature; some responses occur rapidly while others require
 an extended exposure time. However, most of what we know about temperature
 effects comes from studies using constant temperature conditions, which
 are not reflective of natural, fluctuating temperatures. Species with
 temperature-dependent sex determination (TSD) present an ideal system to
 study the temporal aspects of the temperature response because prior
 research has established a number of temperature-responsive genes involved
 in TSD, albeit under constant temperatures. To investigate potential
 differences in the timing of sexual development between constant and
 fluctuating incubation temperatures, we exposed Trachemys scripta embryos
 to two conditions that produce males (constant 26°C and 26 ± 3°C) and two
 that produce females (constant 31°C and 31 ± 3°C), and sampled embryonic
 gonads for gene expression analysis via qPCR.We analyzed three genes
 involved in testis differentiation (Kdm6b, Dmrt1, and Sox9) and two genes
 involved in ovary differentiation (Foxl2 and Cyp19A1). Results show that
 Kdm6b expression was significantly lower under fluctuating temperatures
 compared to constant temperatures. Foxl2 and Cyp19A1 expression were also
 lower under fluctuating temperatures, but not at all stages of
 development. These results suggest that constant temperatures caused
 increases in both Foxl2 and Cyp19A1 expression earlier (developmental
 stage 20) than fluctuating temperatures (stages 22 and 23). Dmrt1 and Sox9
 expression did not differ between constant and fluctuating temperatures.
 These results highlight that not all genes in a temperature-dependent
 process respond to temperature in the same manner. Whether there are
 functional consequences of this variation remains to be determined.
DOI: 10.5061/dryad.3j9kd51jw
title: Selfing rate variation within species is unrelated to life-history traits or geographic range position

description: Premise: In plants, populations and species vary widely along the
 continuum from outcrossing to selfing. Life-history traits and ecological
 circumstances influence among-species variation in selfing rates but their
 general role in explaining intraspecific variation is unknown. Using a
 database of plant species, we test whether life-history traits, geographic
 range position, or abundance predict selfing rate variation among
 populations.  Methods: We identified species where selfing rates
 were estimated in at least three populations at known locations. Two key
 life-history traits (generation time and growth form) were used to predict
 within-species selfing rate variation. Populations sampled within a
 species’ native range were assessed for proximity to the nearest edge and
 abundance. Finally, we conducted linear and segmented regressions to
 determine functional relationships between selfing rate and geographic
 range position within species. Key results: While woody species exhibit
 lower variation in selfing rates compared to herbs, this is explained by
 the lower average selfing rate of woody species. Relationships between
 selfing and peripherality or abundance significantly varied among species
 in their direction and magnitude. However, there was no general pattern of
 increased selfing towards range edges. A power analysis shows that tests
 of this hypothesis require studying many (i.e. 40+) populations.
 Conclusions: Intraspecific variation in plant mating systems is often
 substantial yet remains difficult to explain. Beyond sampling more
 populations, future tests of biogeographic hypotheses will benefit from
 phylogeographic information concerning specific range edges, the study of
 traits influencing mating system (e.g. herkogamy), and measures of
 abundance at local scales (e.g. population density).
description: This dataset contains several files that contain information on
 species and their geographic locations. These data are taken and used by
 an R script, which then generates the results that we report in our
 paper.
description: A user will need to know how to run an R script and how to alter
 the filename paths so that the R script uploads each necessary file at the
 appropriate time.
DOI: 10.5061/dryad.mw6m905xk
title: Data from: Genome-wide investigation of the multiple origins hypothesis for deep-spawning kokanee salmon (Oncorhynchus nerka) across its pan-Pacific distribution

description: Salmonids have emerged as important study systems for investigating
 molecular processes underlying parallel evolution given their tremendous
 life history variation. Kokanee, the resident form of anadromous sockeye
 salmon (Oncorhynchus nerka), have evolved multiple times across the
 species’ pan-Pacific distribution, exhibiting multiple reproductive
 ecotypes including those that spawn in streams, on lake-shores, and at
 lake depths &gt;50 meters. The latter has only been detected in five
 locations in Japan and British Columbia, Canada. Here, we investigated the
 multiple origins hypothesis for deep-spawning kokanee, using 9,721 SNPs
 distributed across the genome analyzed for the vast majority of known
 populations in Japan (Saiko Lake) and Canada (Anderson, Seton, East
 Barrière Lakes) relative to stream-spawning populations in both regions.
 We detected 397 outlier loci, none of which were robustly identified in
 paired-ecotype comparisons in Japan and Canada independently. Bayesian
 clustering and principal components analyses based on neutral loci
 revealed six distinct clusters, largely associated with geography or
 translocation history, rather than ecotype. Moreover, a high level of
 divergence between Canadian and Japanese populations, and between deep-
 and stream-spawning populations regionally, suggest the deep-spawning
 ecotype independently evolved on the two continents. On a finer level,
 Japanese kokanee populations exhibited low estimates of heterozygosity,
 significant levels of inbreeding, and reduced effective population sizes
 relative to Canadian populations, likely associated with transplantation
 history. Along with preliminary evidence for hybridization between
 deep-spawning and stream-spawning ecotypes in Saiko Lake, these findings
 should be considered within the context of on-going kokanee fisheries
 management in Japan.
description: 9021_SNPs_neutral.vcf: genotypic data for 167 individuals at 9021
 SNPs (neutral only) generated via RADseq
 9721_SNPs_all.vcf: genotypic data for 167 individuals at 9721
 SNPs (all) generated via RADseq
 2165_SNPs_neutral_SaikoOnly.vcf: genotypic data for 34 Saiko Lake
 individuals at 2165 SNPs (neutral only) generated via RADseq
 9721_loci_sequences.txt: text file containing sequences for 9721
 loci metadata.txt: individual metadata including sample
 identifiers, location, and ecotype
DOI: 10.5061/dryad.fbg79cnw0
title: Data for: Testing the match-mismatch hypothesis in bighorn sheep in the context of climate change

description: In species with long gestation, females commit to reproduction several
 months before parturition. If cues driving conception date are
 uncoupled from spring conditions, parturition could be mistimed. Mismatch
 may increase with global change if the rate of temporal changes in autumn
 cues differs from the rate of change in spring conditions. Using 17 years
 of data on climate and vegetation phenology, we show that autumn
 temperature and precipitation, but not vegetation phenology, explain
 parturition date in bighorn sheep. Although autumn cues drive the timing
 of conception, they do not predict conditions at parturition in spring. We
 calculated the mismatch between individual parturition date and spring
 green-up, assessed whether mismatch increased over time and investigated
 the consequences of mismatch on lamb neonatal survival, weaning mass and
 overwinter survival. Mismatch fluctuated over time but showed no temporal
 trend. Temporal changes in green-up date did not lead to major fitness
 consequence of mismatch. Detailed data on individually marked
 animals revealed no effect of mismatch on neonatal or overwinter
 survival, but lamb weaning mass was negatively affected by mismatch.
 Capital breeders might be less sensitive to mismatch than income breeders
 because they are less dependent on daily food acquisition. Herbivores in
 seasonal environments may access sufficient forage to sustain lactation
 before or after the spring ‘peak’ green-up, and partly mitigate the
 consequences of a mismatch. Thus, the effect of phenological mismatch on
 fitness may be affected by species life-history, highlighting the
 complexity in quantifying trophic mismatches in the context of climate
 change. 
description: Analytical code for processing data is available
 at https://github.com/larenaud/mismatch. Details on the
 study design is available in Jorgenson, J. T., Festa-Bianchet, M.,
 Lucherini, M., & Wishart, W. D. (1993). Effects of body size,
 population density, and maternal characteristics on age at first
 reproduction in bighorn ewes. Canadian Journal of Zoology, 71(12),
 2509–2517. https://doi.org/10.1139/z93-344
DOI: 10.6078/d1hd9g
title: Course materials and datasets for the Alivisatos group-based undergraduate research program

description: A group-based undergraduate research program (GURP) have been
 developed by the Alivisatos research group at the University of
 California, Berkeley. To assist other groups who may be interested in
 developing their own undergraduate research program, we have deposited
 some materials from our courses here, including raw datasets, lessons, and
 assignments.
DOI: 10.5061/dryad.q2bvq83ks
title: Road salt inputs alter biogeochemistry but not plant community composition in exurban forested wetlands

description: Forested wetlands of the temperate north are increasingly exposed to
 deicing salts, but it is unclear how this may alter wetland
 biogeochemistry and plant community composition. To investigate potential
 effects of deicing salts on exurban forested wetlands in southern New
 England, we employed a multi-site field study to describe spatiotemporal
 patterns of soil physiochemical, water quality, and vegetation
 characteristics with distance from road deicing salt source. We surveyed
 nine road-adjacent, red maple-dominated wetlands to quantify a suite of
 soil parameters (Na+, K+, Mg2+, Ca2+, pH, electrical conductivity (EC),
 heavy metals, N, P, soil moisture), as well as surface and groundwater
 salinity, and vegetation communities. With increasing distance from roads
 along 165-m transects penetrating into each wetland, soil salinity (EC,
 Na+) decreased, while soil base cation concentrations (Mg2+, Ca2+)
 increased, likely due to cation exchange (Na+ displacing other base
 cations). We also measured foliar chemistry and observed elevated Na+ and
 reduced Mg2+ of dominant species leaf tissue near roads, suggesting plant
 nutrient uptake responds to road-salt related changes in soil
 physicochemical variables. Despite this, we did not detect differences in
 plant community composition (ground, shrub layers) along road-salt induced
 soil chemistry gradients in the field, likely because surface and ground
 water salinities were relatively low (maximum: 0.64 ppt). To determine at
 which field salinities we could potentially expect changes in wetland
 plant communities, we conducted a full-factorial, manipulative seed bank
 experiment to examine how NaCl concentration (0, 0.5, 1, 2, 4, 8 parts per
 thousand (ppt)), frequency of salt exposure (pulse, constant) and water
 level (surface, 2-cm below surface) affected soil seed bank responses.
 Seedling richness was reduced at salinities exceeding 1 ppt, and seedling
 density was reduced above 2 ppt, but pulsing tended to alleviate
 salt-induced reductions in seed bank responses. As salinization of
 freshwater ecosystems continues to increase, our results suggest that
 field salinity levels of exurban New England forested wetlands are nearing
 yet still typically below the threshold for which we expect to see strong
 plant community responses.  
description: See Walker et al. for details on data set collection methodology
 and processing
description: Refer to the Walkeretal_readme.txt file for details on how to use
 this data set.
DOI: 10.5061/dryad.g4f4qrfr8
title: Data from: Predicting bushmeat biomass from species composition captured by camera traps: implications for locally-based wildlife monitoring

description: The ‘StatAnalysis.zip’ contains the data and model files. We used it for
 the four analyses below. First, we estimated population densities, the
 mean body mass and camera-trap capture rates of five main bushmeat targets
 in a rainforest of southeast Cameroon: Peters’s duikers (Cephalophus
 callipygus), bay duikers (C. dorsalis), blue duikers (Philantomba
 monticola), brush-tailed porcupines (Atherurus africanus) and Emin’s
 pouched rats (Cricetomys emini). Second, on the basis of the density and
 body mass estimates, we estimated bushmeat biomass—the total biomass of
 the five bushmeat species—and its spatial variation. Third, we calculated
 six bushmeat indicators based on the capture rate estimates. Lastly, we
 examined the correlation between bushmeat biomass and the indicators. The
 ZIP file consists of 16 R script files, three CSV files (in the ‘data’
 subfolder) and 135 stan files (in the ‘stan’ subfolders). It also has two
 empty folders, ‘figure’ and ‘res’, where the figures and R objects of
 model results will be stored following the analyses. Please see the
 document ‘README.txt’ before performing the analysis. This text file gives
 the ZIP file structure and brief descriptions of the files.
description: The two data files—‘DetectionData.csv’ and
 ‘StayTimeData.csv’—were created based on a camera trap study conducted
 from September 2018 to February 2019. The ‘BodyMassData.csv’ contains the
 body mass data of the hunted animals in the study area.
 We estimated population density and its spatial variation using
 the REST model (Nakashima et al. 2018, 2020). The REST model was
 implemented in a Bayesian framework using Stan. We also used Stan to
 estimate the mean body mass and camera-trap capture rates from the
 ‘BodyMassData.csv’ and the 'DetectionData.csv', respectively.
 Finally, bushmeat biomass and bushmeat indicators were calculated using
 the MCMC samples from the WAIC-based optimal models of the density, body
 mass and capture rate estimation.
description: 1. Keep the current folder
 structure. Don't move any files for proper analysis. 2. Please proceed with the analyses
 in the order of the R script file numbers. 3. In each subfolder of the ‘figure’
 and ‘res’ folders, there is a ‘dummy.txt’ file. It is to preserve the
 folder structure. You may remove these text files after
 unzipping.
DOI: 10.5061/dryad.pc866t1pr
title: Japanese chum salmon reproductive traits

description: Geographic clines in life-history traits are often recognized as
 adaptations to the associated transitional environments. As life-history
 traits evolve in response to anthropogenic processes, these geographic
 clines can change over time. The geographic and temporal trends of
 reproductive traits in Japanese chum salmon Oncorhynchus keta were
 analyzed. Data were collected from 23 rivers located between 36° and 45°
 north latitude and 136° and 146° east longitude from 1994 to 2010. We
 confirmed the geographic clines of reproductive traits: relative gonad
 weight increased in more northeasterly locations, and females had fewer,
 but larger, eggs in more northeasterly locations after standardization by
 body size. The geographic clines changed over the years. The northeastward
 geographic trend of increasing gonad weight became more pronounced over
 time. Temporal trends toward smaller but more numerous eggs were evident,
 especially in northeasterly locations. Under natural and sexual selection,
 gonadal investment should be constrained by the energetic demands of the
 cost of migration, particularly in southwesterly locations (which are
 farthest from the feeding grounds), and by breeding competition during
 natural reproduction. In addition, females should have fewer but larger
 eggs owing to constraint on growth opportunities for their offspring in
 more northeasterly regions of Japan, which are colder and have less
 available food. However, global warming may mitigate this constraint on
 growth opportunities in northeastern Japan by increasing river water
 temperatures. Moreover, we consider that relaxation of the effects of
 natural and sexual selection on intense breeding competition and of early
 growth conditions has occurred through domestication selection by hatchery
 programs. These may have caused temporal shifts in geographic clines. We
 should consider several co-occurring anthropogenic impacts on natural and
 sexual selection when evaluating the life-history traits of organisms. For
 the sustainable use of biological resources, maintaining geographically
 adapted life-history traits during adaptation to climate change is
 essential. Therefore, the conservation of wild salmon populations formed
 by natural selection is preferable to the stocking of hatchery-reared fry.
DOI: 10.5061/dryad.tmpg4f50d
title: Data from: Soil mesofauna may buffer the negative effects of drought on alien plant invasion

description: Although many studies have tested the direct effects of drought on alien
 plant invasion, less is known about whether drought affects alien plant
 invasion indirectly via interactions of plants with other groups of
 organisms such as soil mesofauna. To test for such indirect effects, we
 grew single plants of nine naturalized alien target species in
 pot-mesocosms with a community of five native grassland species under four
 combinations of two drought (well-watered vs drought) and two
 soil-mesofauna-inoculation (with vs without) treatments. We found that
 drought decreased the absolute and the relative biomass production of the
 alien plants, and thus reduced their competitive strength in the native
 community. Drought also decreased the abundance of soil mesofauna,
 particularly soil mites, but did not affect the abundance and richness of
 soil herbivores. Soil-fauna inoculation did not affect biomass of the
 alien plants but increased biomass of the native plant community, and
 thereby decreased the relative biomass production of the alien plants.
 This increased invasion resistance due to soil fauna, however, tended (p =
 0.09) to be stronger for plants growing under well-watered conditions than
 under drought. Synthesis. Our multispecies experiment thus shows that soil
 fauna might help native communities to resist alien plant invasions, but
 that this effect might be weakened under drought. In other words, soil
 mesofauna may buffer the negative effects of drought on alien plant
 invasions.
description: All data were collected from a greenhouse expeirment at the
 Northeast Institute of Geography and Agricultural Ecology, Chinese Academy
 of Sciences.
description: The file archives
 'SoilFauna_Drought_PlantInvasion_Date_YJL.tar' include three
 dataset, one named 'SoilFauna_Drought_PlantInvasion.csv'
 (Biomass data), one named 'SoilFaunaData.csv' (Soil Fauna data),
 and one named 'SoilNitrogenData.csv' (soil nitrogen
 data). The file
 'SoilFauna_Drought_PlantInvasion.Rmd' is the R script, and its
 output is 'SoilFauna_Drought_PlantInvasion.html'.
DOI: 10.5061/dryad.xd2547dhm
title: Data from: A camera trap based assessment of climate-driven phenotypic plasticity of seasonal moulting in an endangered carnivore

description: For many species, the ability to rapidly adapt to changes in seasonality
 is essential for long-term survival. In the Arctic, seasonal moulting is a
 key life history event that provides year-round camouflage and thermal
 protection. However, increased seasonal variability can lead to
 phenological mismatch. In this study, we investigated whether winter-white
 (white morph) and winter-brown (blue morph) Arctic foxes (Vulpes lagopus)
 could adjust their winter-to-summer moult to match local environmental
 conditions. We used camera trap images spanning an eight-year period to
 quantify the timing and rate of fur change in a polymorphic subpopulation
 in south-central Norway. Seasonal snow cover duration and temperature
 governed the phenology of the spring moult. We observed a later onset and
 longer moulting duration with decreasing temperature and longer snow
 season. Additionally, white foxes moulted earlier than blue in years with
 shorter periods of snow cover and warmer temperatures. These results
 suggest that phenotypic plasticity allows Arctic foxes to modulate the
 timing and rate of their spring moult as snow conditions and temperatures
 fluctuate. With the Arctic warming at an unprecedented rate, understanding
 the capacity of polar species to physiologically adapt to a changing
 environment is urgently needed in order to develop adaptive conservation
 efforts. Moreover, we provide the first evidence for variations in the
 moulting phenology of blue and white Arctic foxes. Our study underlines
 the different intraspecific selective pressures that can exist in
 populations where several morphs co-occur, and illustrates the importance
 of integrating morph-based differences in future management strategies of
 such polymorphic species.
DOI: 10.34740/kaggle/dsv/14647386
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.25338/b8tw65
title: Stress in paradise: effects of elevated corticosterone on immunity and avian malaria resilience in a Hawaiian passerine

description: Vertebrates confronted with challenging environments often experience an
 increase in circulating glucocorticoids, which result in morphological,
 physiological, and behavioral changes that promote survival. However,
 chronically elevated glucocorticoids can suppress immunity, which may
 increase susceptibility to disease. Since the introduction of avian
 malaria to Hawaii a century ago, low elevation populations
 of Hawaii Amakihi (Chlorodrepanis virens) have undergone
 strong selection by avian malaria and evolved increased resilience (the
 ability to recover from infection), while populations at high elevation
 with few vectors have not undergone selection and remain susceptible. We
 investigated how experimentally elevated corticosterone affects the
 ability of high and low elevation male Amakihi to cope with avian malaria
 by measuring innate immunity, hematocrit, and malaria parasitemia.
 Corticosterone implants resulted in a decrease in hematocrit in high and
 low elevation birds but no changes to circulating natural antibodies or
 leukocytes. Overall, leukocyte count was higher in low than high elevation
 birds. Malaria infections were detected in a subset of low elevation
 birds. Infected individuals with corticosterone implants experienced a
 significant increase in circulating malaria parasites while untreated
 infected birds did not. Our results suggest that Amakihi innate immunity
 measured by natural antibodies and leukocytes is not sensitive to changes
 in corticosterone, and that high circulating corticosterone may reduce the
 ability of Amakihi to cope with infection via its effects on hematocrit
 and malaria parasite load. Understanding how glucocorticoids influence a
 host’s ability to cope with introduced diseases provides new insight into
 the conservation of animals threatened by novel pathogens.
description: The corresponding AMAKIHI_CORT_EXPERIMENT_readme.txt file
 contains information about each variable included in the
 dataset, including units, how it was obtained and/or how it was
 calculated. NA represents data that is not available. Additional
 information about how data was obtained can be found in the corresponding
 manuscript.