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opencc-by-4.0Oct 2016View details →

Supporting data: Prevalence of sexual dimorphism in mammalian phenotypic traits

Supporting material for the manuscript “Prevalence of sexual dimorphism in mammalian phenotypic traits” . This manuscript was published in Nature Communication 26th January 2017

opencc-by-4.0Feb 2017View details →

Dataset 2: All wild type embryo phenotypes from lethal and sub-viable lines scored by DMDD to date (Nov 2016)

The table lists the annotation data from wild type embryos that is the basis of the study. For every annotation the gene symbol, MGI_ID, allele symbol, DMDD_ID, MP term, ID and name is listed. In some cases the same MP term is listed more than once for a specific embryo (DMDD_ID), indicating the phenotypic abnormality was observed more than once in that embryo.

opencc-by-4.0Apr 2024View details →

Soybean Root Phenotype and Genotype Data from the Piney Purdue Agricultural Center (PPAC), Indiana

This data repository contains records of root phenotypes collected in the Pinney Purdue Agricultural Center (PPAC) (Wanatah, Indiana, USA) on 24 soybean genotypes in 2022 along with their genotype information from the intersection of the BARCSoySNP6K and SoySNP50K assays. The repository contains the following files: Bogati_soybean_root_phenotype_data1.xlsx 6k_and_50k_geno.map 6k_and_50k_geno.ped The map file contains chromosome number, SNP ID, Genetic Distance, and Base pair position. The ped file contains sample name (first two columns) with genotype data corresponding to the .map file beginning in column 7.   Acknowledgements:  To-Chia Ting, Luis Vargas, and Sajad Jamshidi assisted in the collection of root phenotype data. Chance Clark helped extract DNA for genotyping.

opencc-by-4.0Sep 2024View details →

Clostridioides difficile in Honduras: a genomic and phenotypic characterization of the persistent RT027 and emergent RT002 genotypes

Supplementary dataset to the manuscript: Clostridioides difficile in Honduras: a genomic and phenotypic characterization of the persistent RT027 and emergent RT002 genotypes, by Mauricio Andino-Molina, Mostafa Abdel-Glil, Fanny Hidalgo-Villeda, Edgardo Tzoc, Gernot Schmoock, Mathias W. Pletz, Heinrich Neubauer & Christian Seyboldt.  Dataset analysed with clostyper (https://gitlab.com/FLI_Bioinfo/clostyper)

opencc-zeroOct 2023View details →

The phenotypic and fitness response to the combination of copper and thermal stressors strongly varies within the ciliate species, Tetrahymena thermophila

Copper pollution can alter biological and trophic functions. Organisms can set up different tolerance strategies, including accumulation mechanisms (intracellular vacuoles, external chelation, etc.) to maintain themselves in copper-polluted environments. Accumulation mechanisms can influence the expression of other phenotypic traits, allowing organisms to improve their fitness. Whether copper effects on accumulation strategies interact with other environmental stressors such as temperature and how this may differ within species are still unsolved questions. Here, we tested experimentally whether the combined effect of copper and temperature modulates traits linked to fitness, morphology, movement and accumulation in six strains of the ciliate Tetrahymena thermophila. We also explored whether copper accumulation might modulate environmental copper concentration effects on phenotypic and fitness traits. Results showed high intraspecific variability in the phenotypic and fitness response to copper, with interactive effects between temperature and copper. In addition, they suggested an attenuation effect of copper accumulation on the sensitivity of traits to copper, but with great variation between strains, temperature and copper concentration. Diversity of responses among strains and their thermal dependencies pleads for the integration of intraspecific variability and multiple stressors approaches in ecotoxicological studies, thus improving the reliability of assessments of the effects of pollutants on biodiversity.

opencc-by-4.0Nov 2023View details →

Phenotypic differences between interfertile Chlamydomonas species- high-resolution confocal z-stacks for visualizing organelle morphology

This repository contains high-resolution confocal z-stacks of two interfertile Chlamydomonas algal species. The protocol to generate this data is described in the associated publication, "Phenotypic differences between interfertile Chlamydomonas species", and briefly summarized here. Cells were collected from agar plates with TAP medium and suspended in 500 µl of liquid TAP medium in a 1.5 ml eppendorf tube overnight. Cells were pelleted using a microcentrifuge at 2000 x g for 2 min and the supernatant removed. For staining mitochondria, PKMito orange was used at a 1:500 concentration and cells were moved to opaque black microcentrifuge tubes and placed on a tube rotator for 45 min. Cells were pelleted again and washed twice with fresh TAP medium. After the final wash and supernatant removal, cells were resuspended in 25 µl of 1.25% low gelling agar in TAP medium (kept at 45 C). Then 1 µl of the cell/agar mixture was mounted on a #1.5 coverslip with a small wax circle drawn to retain the droplet. Coverslips were flipped and placed on a slide and sealed with VALAP. Images were collected on a Nikon CSU W-1 SoRA spinning disk confocal microscope equipped with an ORCA-Fusion BT digital scMOS camera. In order to apply deconvolution in the downstream processing, we needed to oversample (sample beyond Nyquist) in z resolution. To do this, we used a 100×/1.45 NA objective in 2.8× SoRa magnification mode, using ROIs of either 670 × 670 × 81 or 850 × 850 × 91. We imaged with a z-step size of 100 nm for sub-Nyquist sampling. We imaged bright-field first, then 640 nm excitation autofluorescence of chloroplasts, and then 561 nm excitation for PKmito orange dye, because the chloroplasts would bleach after 561 nm excitation. We set exposures to 300 ms with 30% and 50% laser power for 640 and 561, respectively.We have included a set of demo data (10 images per species) that accompany the pub hosted on the Arcadia Science webpage (3Dmorpho_demo_data). In addition, we included all of the raw data we collected in this experiment (3Dmorpho_raw_data). Please use the point spread functions (PSF) from the zipped folders for each respective dataset (demo or raw).

opencc-zeroNov 2023View details →

Data for: Phenotypic adaptation to temperature in the mosquito vector, Aedes aegypti

Most models exploring the effects of climate change on mosquito-borne disease ignore thermal adaptation. However, if local adaptation leads to changes in mosquito thermal responses, 'one size fits all' models could fail to capture current variation between populations and future adaptive responses to changes in temperature. Here we assess phenotypic adaptation to temperature in Aedes aegypti, the primary vector of dengue, Zika, and chikungunya viruses. First, to explore whether there is any difference in existing thermal response of mosquitoes between populations we used a thermal knockdown assay to examine five populations of Ae. aegypti collected from climatically diverse locations in Mexico, together with a longstanding laboratory strain. We identified significant phenotypic variation in thermal tolerance between populations. Next, to explore whether such variation can be generated by differences in temperature we conducted an experimental passage study by establishing six replicate lines from a single field-derived population of Ae. aegypti from Mexico, maintaining half at 27°C and the other half at 31°C. After 10 generations we found a significant difference in mosquito performance, with the lines maintained under elevated temperatures showing greater thermal tolerance. Moreover, these differences in thermal tolerance translated to shifts in the thermal performance curves for multiple life history traits, leading to differences in overall fitness. Together, these novel findings provide compelling evidence that Ae. aegypti populations can and do differ in thermal response, suggesting that simplified thermal performance models might be insufficient for predicting the effects of climate on vector-borne disease transmission.

opencc-zeroNov 2023View details →

Phenotypic plasticity determines differences between the skulls of tigers from mainland Asia

Tiger subspecific taxonomy is controversial because of morphological and genetic variation found between now fragmented populations, yet the extent to which phenotypic plasticity or genetic variation affects phenotypes of putative tiger subspecies has not been explicitly addressed. In order to assess the role of phenotypic plasticity in determining skull variation, we compared skull morphology amongst continental tigers from zoos and the wild. In turn, we examine continental tiger skulls from across their wild range, to evaluate how the different environmental conditions experienced by individuals in the wild can influence morphological variation. Fifty-seven measurements from 172 specimens were used to analyse size and shape differences amongst wild and captive continental tiger skulls. Captive specimens have broader skulls, and shorter rostral depths and mandible heights than wild specimens. In addition, sagittal crest size is larger in wild Amur tigers compared with those from captivity, and it is larger in wild Amur tigers compared to other wild continental tigers. The degree of phenotypic plasticity shown by the sagittal crest, skull width, and rostral height suggests that the distinctive shape of Amur tiger skulls compared with that of other continental tigers is mostly a phenotypically plastic response to differences in their environments.

opencc-by-4.0Nov 2023View details →

Phenotypic stasis despite genetic divergence and differentiation in Caenorhabditis elegans.

# Data for the manuscript : Phenotypic stasis despite genetic divergence and differentiation in Caenorhabditis elegans.https://doi.org/10.1101/2022.05.28.493856 The data directory contains:- the raw transition rates in  Final_merged_data_NGM.txt- population male frequencies estimates : population_rep_male_freqs.txt- fertility data from the Cemee: fertility.rda (from Noble et al. 2017)- Mean state frequencies in the movies : State_freq_NGM.txt The Rcode directory contains all code to reproduce the analysis is available on github:https://github.com/ExpEvolWormLab/Mallard_Stasis

opencc-zeroNov 2023View details →

Differences in phenotypic variance between old and young congeneric species on a small island

Aim: Insular environments theoretically promote within-species phenotypic variance, in part but not only because insular species enjoy a lower number of trophic interactions than their mainland counterparts. However, environmental factors apparently confound empirical comparisons between insular and mainland systems. To address this issue, we studied sympatric, congeneric species from the same small island, but that stemmed from separate colonization events. We predicted that the time since the species had colonized the island would correlate positively with the within-species variance in morphometrics. Location: Lifu Island, New Caledonia, South Pacific. Taxa: Zosterops inornatus, Z. minutus, Z. lateralis (Passeriformes). Methods: We measured 7 morphological traits and used principal component analysis to compute axes of variation. Results: The within-species variance in bill size and in feet/tail ratio corrected for body size increased with the estimated time since the species had been on the island. A similar but nonsignificant trend existed for body size and bill width. Main conclusions: The morphometrics of the three species of Zosterops birds from Lifu supported the hypothesis that insular environments promote within-species phenotypic variance, and cast a new light on the role of competition in the erosion of phenotypic variance.

opencc-zeroDec 2023View details →

Group phenotypic composition drives task performances in ants

Differences in individual behaviour within a group can give rise to functional dissimilarities between groups, particularly in social animals. However, how individual behavioural phenotypes translate into the group phenotype remains unclear. Here we investigate whether individual behavioural type affects group performance in an eusocial species, the ant Aphaenogaster senilis. We measured individual behavioural traits and created groups of workers with similar behavioural type, either high-exploratory or low-exploratory. We tested these groups in four different, ecologically relevant tasks: reaction to an intruder, prey retrieval from a maze, nest relocation and tool use. We show that, compared to groups of low-exploratory workers, groups of high-exploratory workers were more aggressive towards intruders, more efficient in collecting prey, faster in nest relocation and more likely to perform tool use. Our results demonstrate a strong link between individual and collective behaviour in ants. This supports the 'behavioural type hypothesis' for group dynamics, which suggests that an individual's behaviour in a social environment reflects its own behavioural type. The average behavioural phenotype of a group can therefore be predicted from the behavioural types of individual group members.

opencc-zeroJan 2024View details →

Genetic differentiation and phenotypic plasticity drive troglomorphic character development in European cavefish

The Aach cave loach (Barbatula barbatula), a recently discovered member of the Nemacheilidae family, offers a unique opportunity to understand the mechanisms underlying evolutionary change. In a common garden experiment, we reared groups of laboratory-bred cave, surface, and hybrid loach under different light conditions. Troglomorphic characters varied significantly among the fish, influenced to a different extent by parental origin and light conditions. Cavefish progeny consistently exhibited smaller eyes, lighter pigmentation, longer barbels, and larger olfactory epithelia than surface fish, while hybrids displayed intermediate characteristics. Surface and hybrid fish raised in complete darkness resembled the cavefish phenotype, while cavefish raised under a natural photoperiod approached the surface form. Characters associated with eye degeneration were found to be primarily heritable. Conversely, traits related to chemo- and mechano-reception were enhanced in the surface and hybrid groups reared in complete darkness, suggesting phenotypic plasticity. Our findings offer valuable insights into the interplay between genetic differentiation and phenotypic plasticity to troglomorphic adaption. This contributes to the broader understanding of the early stages of adaptation, where phenotypic plasticity, drift, and selection shape phenotypes. Relatively recently established cavefish, such as the Aach cave loach, are promising candidates for comparative research investigating evolutionary mechanisms.

opencc-by-4.0Jan 2024View details →

Supplementary data for Inter-provenance variability and phenotypic plasticity of wood and leaf traits related to hydraulic safety and efficiency in seven European beech (Fagus sylvatica L.) provenances differing in yield

Dataset and supplementary file for Inter-provenance variability and phenotypic plasticity of wood and leaf traits related to hydraulic safety and efficiency in seven European beech (Fagus sylvatica L.) provenances differing in yield paper. The ANFS_data file includes individual level measurements of xylem safety and efficiency traits, leaf traits and growth among 7 provenances planted at two common garden sites in Germany and Slovakia. More details related to the methodology might be found in the published paper by Kurjak et al. 2024. The ANFS_supplementary file includes the test for differences in distance to tip between sites and provenances,  based on the branch diameter-branch length scaling.

opencc-zeroFeb 2024View details →

Phenotypic traits of 17 populations of Spartina alterniflora in China

Understanding the ecological and evolutionary processes that underlie phenotypic and genetic variation among invasive plant populations and the capacity of such populations to colonize a broad range of environments is a major goal in ecology. Rapid adaptation to local environmental conditions often leads to latitudinal clines in both phenotypes and genotypes of invasive plant species. Previous studies suggest that natural selection influenced a latitudinal cline in phenotypic traits of the invasive plant Spartina alterniflora in China. However, little is understood of the relationship between genetic and phenotypic differentiation and environmental factors among S. alterniflora populations. Here, we studied whether S. alterniflora exhibits a latitudinal cline in genetic diversity across the east coast of China and whether genetic and phenotypic differentiation among populations were correlated with environmental factors. The Restriction-site Associated DNA (RAD-seq) sequencing was used to obtained genomic information of 17 populations of S. alterniflora in China. A redundancy analysis (RDA) was performed to assess whether environmental variables were corelated with genetic and phenotypic differentiation among the populations. A univariate environmental association analysis (implemented through Latent Factor Mixed Model; LFMM) and a principal component analysis (PCAdapt) were used to test for signature of local adaptation. A total of 3, 310 SNPs showed a clear genetic structure among populations in three climatic regions (northern, mid-latitude and southern). Positive correlations between genetic differentiation and variation in reproductive characteristics of S. alterniflora were revealed, suggesting that sexual reproduction traits might be stable and genetically heritable. Outlier loci that were identified by both PCAdapt and LFMM methods were significantly correlated to soil phosphorus content, soil salinity, and precipitation. These results provide evidence of molecular signatures of local adaptation of S. alterniflora and suggest that rapid adaptive evolution may facilitate invasiveness of S. alterniflora in China.

opencc-by-4.0Mar 2024View details →

Investigating the causal association between immune cell phenotypes and allergic diseases and non-allergic asthma using conventional Two-sample and Bayesian weighted Mendelian randomization

Investigating the causal association between immune cell phenotypes and allergic diseases and non-allergic asthma using conventional Two-sample and Bayesian weighted Mendelian randomization

Data from: Biomass yield, yield components and growing season phenotypic measurements of Miscanthus

For sustainable biomass production of Miscanthus × giganteus (hereafter miscanthus), understanding the impact of stand age and nitrogen (N) fertilization on biomass yield is crucial. This study investigated the effects of varying N fertilization rates (0, 56, 112, and 168 kg N ha-1) on yield components (tiller height, density, and weight) and their correlations with end-of-season biomass yield in miscanthus. We also explored end-of-season biomass yield prediction using in-season traits (canopy height, leaf area index (LAI), and leaf chlorophyll content (LCC)). The study was conducted at two sites in Illinois: a previously unfertilized 10-year-old miscanthus research stand at Urbana and a 16-year-old commercial stand at Pesotum with a history of annual 56N application. Results from 2018-2021 in Urbana and 2020-2021 in Pesotum showed increased biomass yields with N fertilization, varying by rate, year, and location. Biomass yield in Pesotum peaked at 56N, while in Urbana, it increased significantly at 112 kg N ha-1. Biomass yield was strongly correlated with tiller height and weight measured at Urbana across N rates. Morphological traits measured every 2-3 weeks during the 2020 and 2021 growing seasons showed that canopy height was the strongest single predictor of miscanthus biomass yield, followed by LCC. Mid-August to September measurements of these traits were the best predictors of biomass yield. Multiple regressions involving the canopy height and LCC further improved yield predictions. We conclude that while N enhances biomass yields of aging miscanthus, the optimum rate depends on the site, environmental conditions, and management.

Data from: Phenotypic resources immortalized in a panel of wild-derived strains of five species of house mice

The house mouse, Mus musculus, is a widely used animal model in biomedical research, with classical laboratory strains (CLS) being the most frequently employed. However, the limited genetic variability in CLS hinders their applicability in evolutionary studies. Wild-derived strains (WDS), on the other hand, provide a suitable resource for such investigations. To assess the proportion of variation added by wild progenitors, we estimated phenotypic variation in 84 WDS representing 5 species (M. musculus, M. spretus, M. spicilegus, M. macedonicus, M. caroli), 3 subspecies (M. m. musculus, M. m. domesticus, M. m. castaneus), and compared it with 5 CLS. The spectrum of WDS captures long-term mouse evolution, estimated to be over 5 million years ago since the split of M. caroli from the remaining mouse species. All mice are housed in a conventional breeding facility (without a nanofilter barrier or specific-pathogen free condition) at the Institute of Vertebrate Biology, Czech Academy of Sciences, in Studenec. They are maintained under standard conditions: light/dark regime of 14/10 hours, temperatures of 23 ± 1 °C during summer (April-September) and 22 ± 1 °C during winter (October-March), respectively, and relative humidity within 40-70 %. Mice have access to food pellets and tap water ad libitum. Further data on this mouse repository and WDS can be obtained at <a href="https://housemice.cz/en/strains/">https://housemice.cz/en/strains/</a>. Morphological traits were measured in 4335 mice and include body weight, spleen weight, body length, tail length, weight of both ovaries, sperm count, the weight of testes, left epididymis, and seminal vesicles. Reproductive ability was estimated in 87 WDS and 8 CLS. This dataset was obtained from 90,077 offspring born to 8,298 mothers in 17,049 litters recorded in Studenec studbooks between 2000 and 2023. Reproductive performance was characterized by litter size, newborn mortality (calculated as the proportion of stillborn or cannibalized mice across all litters), and the number of generations produced per year. We also estimated the time since a WDS was established from wild progenitors until completing 20 generations of strict brother-sister mating, i.e., the generation at which a strain of mice can be considered inbred. Although CLS resemble M. m. domesticus and M. m. musculus WDS, they differ from them in 8 and 11 out of 15 phenotypic traits, respectively. The data suggest that WDS can be a useful tool in evolutionary studies, providing a basis for comparative analyses with other mammal taxa, particularly classical laboratory mice. The detected stunning phenotypic variation supplemented by genetic variation have great potential for medical applications.

Data from: Historical field records reveal habitat as an ecological correlate of locomotor phenotypic diversity in the radiation of Neotropical Geophagini fishes

Phenotypic macroevolutionary studies provide insight into how ecological processes shape biodiversity. However, the complexity of phenotype-ecology relationships underscores the importance of also validating phenotype-based ecological inference with direct evidence of resource use. Unfortunately, macroevolutionary scale ecological studies are often hindered by the challenges of acquiring taxonomically and spatially representative ecological data for large and widely distributed clades. The South American cichlid fish tribe Geophagini represents a continentally distributed radiation whose early locomotor morphological divergence suggests habitat as one ecological correlate of diversification, but an association between locomotor traits and habitat preference has not been corroborated. Field notes accumulated over decades of collecting across South America provide first-hand environmental records that can be mined for habitat data in support of macroevolutionary ecological research. In this study, we applied a newly developed method to transform descriptive field note information into quantitative habitat data, and used it to assess habitat preference and its relationship to locomotor morphology in Geophagini. Field note-derived data shed light on geophagine habitat use patterns and reinforced habitat as an ecological correlate of locomotor morphological diversity. Our work emphasizes the rich data potential of museum collections, including often overlooked material such as field notes, for evolutionary and ecological research.

Supplementary material: CYB561 supports the neuroendocrine phenotype in castration-resistant prostate cancer

Castration-resistant prostate cancer (CRPC) is associated with resistance to androgen deprivation therapy, and an increase in the population of neuroendocrine (NE) differentiated cells. It is hypothesized that NE differentiated cells secrete neuropeptides that support androgen-independent tumor growth and induce aggressiveness of adjacent proliferating tumor cells through a paracrine mechanism. The cytochrome b561 (CYB561) gene, which codes for a secretory vesicle transmembrane protein, is constitutively expressed in NE cells and highly expressed in CRPC. CYB561 is involved in the α-amidation-dependent activation of neuropeptides and contributes to regulating iron metabolism which is often dysregulated in cancer. These findings led us to hypothesize that CYB561 may be a key player in the NE differentiation process that drives the progression and maintenance of the highly aggressive NE phenotype in CRPC. In our study, we found that CYB561 expression is upregulated in metastatic and NE prostate cancer (NEPC) tumors and cell lines compared to normal prostate epithelia and that its expression is independent of androgen regulation. Knockdown of CYB561 in androgen-deprived LNCaP cells dampened NE differentiation potential and transdifferentiation-induced increase in iron levels. In NEPC PC-3 cells, depletion of CYB561 reduced the secretion of growth-promoting factors, lowered intracellular ferrous iron concentration, and mitigated the highly aggressive nature of these cells in complementary assays for cancer hallmarks. These findings demonstrate the role of CYB561 in facilitating transdifferentiation and maintenance of NE phenotype in CRPC through its involvement in neuropeptide biosynthesis and iron metabolism pathways.