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opencc-by-4.0Nov 2024View details →

DeepCanola: Phenotyping Brassica Pods Using Semi-Synthetic Data and Active Learning

Dataset accomapnying the publication: DeepCanola: Phenotyping Brassica Pods Using Semi-Synthetic Data and Active Learning by Van Vliet, Atkins et al. We provide model weights, training and vlidation datasets, as well as phenotype outputs. Each file/folder is outlined below: <ul> <li>deepcanola.pth - Model weights for the final Model 4, named DeepCanola</li> <li>generated_datasets - Datasets generated at each stage of the active learning process, datasets 1-4 <ul> <li>Each folder is an iteration of the active learning process, inside each folder are the generated images and associated annotations stored in the COCO format.</li> </ul> </li> <li>real_world_datasets - Real-world datasets used for either creation of the pod pools or validation. Datasets include: <ul> <li>br9 - Ordered and disordered dataset of images with generated pod length data of the ordered images stored in the `br9_gt_lengths.csv` file</li> <li>br11 - Ordered and disordered dataset of images only</li> <li>br17 - Ordered dataset with ground-truth of images with length annotations collected in ImageJ and stored in the `BR017 POD SCAN DATA.csv` file.</li> <li>misc - Dataset of miscellaneous images including Brassica napus from Rothamstead and brassica relatives</li> </ul> </li> <li>data_generation_pools - Pools used to generate semi-synthetic data at each step of the active learning process. Pools include: <ul> <li>background_pool - Created background images to be selected at random by the semi-synthetic data generation script</li> <li>pod_pools - Pools of pods used in the semi-synthetic data generation process. Pod pools include: <ul> <li>br9 - 673 pods with associated masks</li> <li>br9 and br17 - 673 + 332 pods with associated masks</li> </ul> </li> </ul> </li> <li>deepcanola_outputs - Phenotype data outputs generated by DeepCanola. Each output is stored as a .csv file of both length measurements of each pod (with _objects.csv suffix), and average length measurements per image (with _averages.csv suffix). Outputs include: <ul> <li>br9_ordered</li> <li>br9_disordered</li> <li>br17</li> </ul> </li> </ul>

opencc-by-4.0May 2024View details →

Code and Data for manuscript "Floral phenotypic divergence and genomic insights in an Ophrys orchid: Unraveling early speciation processes"

Floral phenotypic divergence and genomic insights in an Ophrys orchid: Unraveling early speciation -------- This repository contains all the R code used in the manuscript: * Title: "Floral phenotypic divergence and genomic insights in an Ophrys orchid: Unraveling early speciation" * Authors: Anais Gibert, Schatz Bertrand, Buscail Roselyn, Dominique Nguyen, Baguette Michel, Bartes Nicolas and Joris Bertrand * Year of publication: 2024 * doi: https://doi.org/10.1101/2024.03.21.586062   Synopsis of the study -------- <ul> <li> Adaptive radiation in Ophrys orchids leads to complex floral phenotypes that vary in scent, color and shape. </li> <li> Using a novel pipeline to quantify these phenotypes, we investigated trait divergence at early stages of speciation in six populations of Ophrys aveyronensis experiencing recent allopatry. By integrating different genetic/genomic techniques, we investigated: (i) variation and integration of floral components (scent, color and shape), (ii) phenotypes and genomic regions under divergent selection, and (iii) the genomic bases of trait variation. </li> <li> We identified a large genomic island of divergence, associated with phenotypic variation in particular in floral odor. We detected potential divergent selection on macular color, while convergent selection was suspected on floral morphology and for several volatile olfactive compounds. We also identify candidate genes involved in anthocyanin and in steroid biosynthesis pathways associated with standing genetic variation in color and odor. </li> <li> This study sheds light on early differentiation in Ophrys, revealing patterns that often become invisible over time, i.e., the geographic mosaic of traits under selection and the early appearance of strong genomic divergence. It also supports a crucial genomic region for future investigation and highlights the value of a multifaceted approach in unraveling speciation within taxa with large genomes. </li> </ul>   Running the code -------- Here we present the data and code for carrying out the analyses, as well as the figures and tables from the article and the supplementary material. Once you have installed the necessary packages, run the commands in 'analysis_share.R'. This script uses several functions available in the '/R' directory. Figures and tables are produced in a 'manuscript/figures' and 'manuscript/tables' directory.  The `/data' directory contains the data used in the analyses (data/input or data/output), but also the resulting datasets produced by the code (data/RData/).

opencc-zeroNov 2021View details →

Phenological data for the article: Phenotypic plasticity drives phenological changes in a Mediterranean blue tit population

Earlier phenology induced by climate change, such as the passerines' breeding time, is observed in many natural populations. Understanding the nature of such changes is key to predict the responses of wild populations to climate change. Genetic changes have been rarely investigated for laying date, though it has been shown to be heritable and under directional selection, suggesting that the trait could evolve. In a Corsican blue tit population, the birds' laying date has significantly advanced over 40 years, and we here determine whether this response is of plastic or evolutionary origin, by comparing the predictions of the breeder's and the Robertson-Price (STS) equations, to the observed genetic changes. We compare the results obtained for two fitness proxies (fledgling and recruitment success), using models accounting for their zero-inflation. Because the trait appears heritable and under directional selection, the breeder's equation predicts that genetic changes could drive a significant part of the phenological change observed. We however found that fitness proxies and laying date are not genetically correlated. The STS therefore predicts no evolution of the breeding time, predicting correctly the absence of trend in breeding values. Our results also emphasize that when investigating selection on a plastic trait under fluctuating selection, part of the fitness-trait phenotypic covariance can be due to within individual covariance. In the case of repeated measurements, splitting within and between individual covariance can shift our perspective on the actual intensity of selection over multiple selection episodes, shedding light on the potential for the trait to evolve.

opencc-zeroDec 2021View details →

Data from: Genomic region associated with run-timing has similar haplotypes and phenotypic effects across three lineages of Chinook salmon

Conserving life history variation is a stated goal of many management programs, but the most effective means by which to accomplish this are often far from clear. Early, premature migrating and late, mature migrating forms of Chinook salmon face unequal pressure from natural and anthropogenic forces. These forces may result in the diminishment of migration variation in some stocks because migration timing is known to be highly heritable. Genomic regions of chromosome 28 are known to be strongly associated with migration variation in adult Chinook salmon, but it remains unclear whether there is consistent association among the diverse populations of Chinook salmon. Therefore, application of this association for management may be premature. We examined the association of genetic variation in 28 markers on chromosome 28 surveyed with high-throughout genotyping (GT-seq) with individual run timing characteristics gleaned from passive integrated transponder recordings of over 5,000 Chinook salmon from the three phylogeographic lineages that inhabit the Columbia River Basin. Despite the strong genetic differences among them, the three lineages exhibited very similar genetic variants in the chromosome 28 region and moderate to strong association of these variants and run timing phenotypes. This is particularly notable for the interior stream-type lineage, which exhibits an earlier and more constrained migration of fish than the other lineages and which are exclusively premature when they enter freshwater. In both interior stream-type and interior-ocean type Chinook salmon, heterozygotes of the most strongly associated linkage groups are largely intermediate to homozygotes in migration timing, and while we make no robust conclusions about dominance, results indicate codominance or marginal partial dominance of the early migrating allele. Our results lend support to the cautious utilization of chromosome 28 variation in tracking and predicting run timing in these Chinook salmon.

Figure 6 in Molecular and phenotypic data reveal a new Amazonian species of pit vipers (Serpentes: Viperidae: Bothrops)

Figure 6. Geographic map of South America showing the distribution of Bothrops oligobalius sp. nov. (yellow) and B. brazili (red). Outlined diamonds and circles represent sites with genetic samples available. Diamonds with an inner dot indicate the type locality of each both species. The Amazonian biome is highlighted in green; the Amazon River is also indicated. Photos: B. oligobalius sp. nov. from French Guiana, by Maël Dewynter; B. brazili from Porto Velho, RO, Brazil, by FDV.

Figure 3 in Molecular and phenotypic data reveal a new Amazonian species of pit vipers (Serpentes: Viperidae: Bothrops)

Figure 3. Holotype of Bothrops oligobalius sp. nov. (MZUSP 23282, field number MTR 13844), from Lourenço Municipality, State of Amapá, Brazil. A: Dorsal view; B: Ventral view. Scale bar = 1 cm.

Figure 8 in Molecular and phenotypic data reveal a new Amazonian species of pit vipers (Serpentes: Viperidae: Bothrops)

Figure 8. Bothrops brazili in dorsal view. A- DHMECN3035 from Ecuador B- QCAZ4827 from Pastaza, Ecuador. Scale bar = 1 cm.

Figure 4 in Molecular and phenotypic data reveal a new Amazonian species of pit vipers (Serpentes: Viperidae: Bothrops)

Figure 4. Head of the holotype (MZUSP 23282) of Bothrops oligobalius sp. nov. in (a) lateral, (b) dorsal and (c) ventral views. Scale bar 1 cm.

opencc-zeroDec 2021View details →

Genomic data from: Are you ready for the heat? Phenotypic plasticity vs adaptation of heat tolerance in three-spined stickleback

Heat waves constitute a challenge for aquatic ectotherms. However, the thermal tolerance of animals and their individual phenotypic plasticity to respond to heat waves may be influenced by thermal history. We tested these hypotheses by comparing the upper thermal tolerance and the individual capacities of three-spined sticklebacks from populations with different thermal histories to respond to heat waves. Two populations originated from thermally polluted nuclear power plant (NPP) habitats, while four locations represented geographically adjacent control areas. To disentangle the genetic adaptation from the phenotypic plastic response, we measured the individual upper thermal tolerance and the responses at molecular level in common garden conditions before and after a laboratory-mimicked heat wave. We found that the sticklebacks exhibit considerable phenotypic plasticity in thermal tolerance since the heat wave increased fish upper thermal tolerance significantly. The individual plasticity to respond to the heat wave was also negatively correlated to initial thermal tolerance. On the other hand, neither the thermal tolerance nor the plastic responses differed between NPP and control sites despite detection of significant but low genome-wide divergence in 10 out of 15 pairwise comparisons. Our results suggest that five decades of nuclear power plant activity with warmer water has not resulted in a detectable evolutionary change in either the upper thermal tolerance or its plasticity in three-spined sticklebacks potentially rendering them sensitive to frequent heat waves.

opencc-by-4.0Jan 2022View details →

Data for manuscript on objective phenotyping of alfalfa roots

These are images for the manuscript, "Objective phenotyping of root system architecture using image augmentation and machine learning in alfalfa." Alfalfa_root_ML_segmented.zip contains the root images segmented from the background using RootPainter and that were used as input for RhizoVision Explorer. Alfalfa_root_ML_color_photographs.zip contains the original color photographs of the roots, except that the circular scale and ID tag have been cropped out and filled with black to aid image analysis.

opencc-zeroJan 2022View details →

Phenotypic data for M. edulis responses to warming and ocean acidification

1. In mosaic marine habitats, such as intertidal zones, ocean acidification (OA) is exacerbated by high variability of pH, temperature, and biological CO2 production. The non-linear interactions among these drivers can be context-specific and their effect on organisms in these habitats remains largely unknown, warranting further investigation. 2. We were particularly interested in Mytilus edulis (the blue mussel) from intertidal zones of the Gulf of Maine (GOM), USA for this study. GOM is a hot spot of global climate change (average Sea Surface Temperature (SST) increasing by > 0.2 °C y−1 ) with > 60% decline in mussel population over the past 40 years. 3. Here, we utilize bioenergetic underpinnings to identify limits of stress tolerance in M. edulis from GOM exposed to warming and OA. We have measured whole-organism oxygen consumption rates and metabolic biomarkers in mussels exposed to control and elevated temperatures (10 vs. 15 °C, respectively) and current and moderately elevated PCO2 levels (~ 400 vs. 800 µatm, respectively). 4. Our study demonstrates that adult M. edulis from GOM are metabolically resilient to the moderate OA scenario but responsive to warming as seen in changes in metabolic rate, energy reserves (total lipids), metabolite profiles (glucose and osmolyte dimethyl amine) and enzyme activities (carbonic anhydrase and calcium-ATPase). 5. Our results are in agreement with recent literature that OA scenarios for the next 100-300 years do not affect this species, possibly as a consequence of maintaining its in vivo acid−base balance.

opencc-zeroFeb 2022View details →

Data from: Rich resource environment of fish farms facilitates phenotypic variation and virulence in an opportunistic fish pathogen

Phenotypic variation is suggested to facilitate the persistence of environmentally growing pathogens under environmental change. Here we hypothesized that the intensive farming environment induces higher phenotypic variation in microbial pathogens than natural environment, because of high stochasticity for growth and stronger survival selection compared to the natural environment. We tested the hypothesis with an opportunistic fish pathogen Flavobacterium columnare isolated either from fish farms or from natural waters. We measured growth parameters of two morphotypes from all isolates in different resource concentrations and two temperatures relevant for the occurrence of disease epidemics at farms and tested their virulence using a zebrafish (Danio rerio) infection model. According to our hypothesis, isolates originating from the fish farms had higher phenotypic variation in growth between the morphotypes than the isolates from natural waters. The difference was more pronounced in higher resource concentrations and the higher temperature, suggesting that phenotypic variation is driven by the exploitation of increased outside-host resources at farms. Phenotypic variation of virulence was not observed based on isolate origin but only based on morphotype. However, when in contact with the larger fish, the less virulent morphotype of some of the isolates also had high virulence. As the less virulent morphotype also had higher growth rate in outside-host resources, the results suggest that both morphotypes can contribute to F. columnare epidemics at fish farms, especially with current prospects of warming temperatures. Our results suggest that higher phenotypic variation per se does not lead to higher virulence, but that environmental conditions at fish farms could select isolates with high phenotypic variation in bacterial population and hence affect evolution in F. columnare at fish farms. Our results highlight the multifaceted effects of human-induced environmental alterations in shaping epidemiology and evolution in microbial pathogens.

opencc-zeroMar 2022View details →

Phenotype data for: Pleiotropic and non-redundant effects of an auxin importer in Setaria and maize

Directional transport of auxin is critical for inflorescence and floral development in flowering plants, but the role of auxin influx carriers (AUX1 proteins) has been largely overlooked. Taking advantage of available AUX1 mutants in Setaria viridis and maize, we uncover previously unreported aspects of plant development that are affected by auxin influx, including higher order branches in the inflorescence, stigma branch number, and glume (floral bract) development, and plant fertility. However, disruption of auxin flux does not affect all parts of the plant, with little obvious effect on inflorescence meristem size, time to flowering, and anther morphology. In double mutant studies in maize, disruptions of ZmAUX1 also affect vegetative development. A GFP-tagged construct of Spp1 under its native promoter showed that the SPP1 protein localizes to the plasma membrane of outer tissue layers in both roots and inflorescences, and accumulates specifically in inflorescence branch meristems, consistent with the mutant phenotype and expected auxin maxima. RNA-seq analysis finds that most gene expression modules are conserved between mutant and wildtype plants, with only a few hundred genes differentially expressed in spp1 inflorescences. Using CRISPR-Cas9 technology, we disrupted SPP1 and the other four AUX1 homologs in S. viridis. SPP1 has a larger effect on inflorescence development than the others, although all contribute to plant height, tiller formation, leaf, and root development. The AUX1 importers are thus not fully redundant in S. viridis. Our detailed phenotypic characterization plus a stable GFP-tagged line offer tools for future dissection of the function of auxin influx proteins.

opencc-zeroApr 2022View details →

Data from: Competitive consequences determined by phenotypic but not genetic distance: a study with asexual Daphnia genotypes

1. How evolutionary relatedness influences the strength of competitive interactions among genetically isolated populations has been a long-standing interest in ecology. Darwin's "Competition Relatedness Hypothesis (CRH)" states that, since closely related species should compete more strongly, they are less likely to coexist, while Herbert's "Bimodal Competition Hypothesis (BCH)" predicts that competitive exclusion is less likely to occur when the competing species are genetically close or distant. 2. To test these hypotheses, we experimentally examined the difference in the competitive ability and life tables of fecundity and survivorship among four different genotypes of asexual Daphnia cf. pulex that diverged from a single ancestral genotype. 3. The experiments showed that the competitive consequences differed depending on the pairing of the competing genotypes, and that the degree of the competitive exclusion was lower when the competing genotypes were genetically closer to each other. These results partially supported the BCH but not the CRH at all. More importantly, the degree of competitive exclusion was better predicted by the phenotypic rather than genetic distances between the competing genotypes. 4. The life table experiments revealed that competitively inferior genotypes had higher early reproduction rates, but survival rates decreased with age and thus body size, probably a result of selection by predation pressures found in nature. 5. These results indicate that competitive superiority is highly dependent on selection pressures that given organisms have been evolutionally subjected to, and, that genetic similarity is not necessarily an appropriate measure for predicting the completive exclusion on an ecological time scale. To predict competitive relationships among the organisms, it is essential to comprehend their phenotypic differences rather than simply knowing their genetic or phylogenetic relationships.

opencc-zeroJun 2022View details →

Data for: Anti-predator phenotype in crucian carp altered by a psychoactive drug

Predator-inducible defences constitute a widespread form of adaptive phenotypic plasticity, and such defences have recently been suggested linked with the neuroendocrine system. The neuroendocrine system is a target of endocrine disruptors, such as psychoactive pharmaceuticals, which are common aquatic contaminants. We hypothesized that exposure to an antidepressant pollutant, fluoxetine, influences the physiological stress response in our model species, crucian carp, affecting its behavioural and morphological responses to predation threat. We examined short- and long-term effects of fluoxetine and predator exposure on behaviour and morphology in crucian carp. 17 days of exposure to a high dose of fluoxetine (100 µg L-1), resulted in a shyer phenotype, regardless of the presence/absence of a pike predator, but this effect disappeared after long-term exposure. Fluoxetine effects on morphological plasticity was context dependent as a low dose (1 µg L-1) only influenced crucian carp body shape in pike presence. A high dose of fluoxetine strongly influenced body shape regardless of predator treatment. Our results highlight that environmental pollution by pharmaceuticals could disrupt physiological regulation of ecologically important inducible defences.

opencc-zeroJun 2022View details →

Data for: Phenotypic senescence in a natural insect population

Senescence seems to be universal in living organisms and plays a major role in life-history strategies. Phenotypic senescence, the decline of body condition and/or performance with age, is a largely understudied component of senescence in natural insect populations, although it would be important to understand how and why insects age under natural conditions. We aimed (i) to investigate how body mass and thorax width change with age in a natural population of the univoltine Clouded Apollo butterfly (Parnassius mnemosyne, Lepidoptera: Papilionidae) and (ii) to assess the relationship of this change with sex and wing length. We studied a population between 2014 and 2020 using mark-recapture during the whole flight period each year. Repeated measurements of body mass and thorax width and single measurements of wing length were performed on marked individuals. We analysed body mass and thorax width change with age (days since marking), wing length and the date of the first capture. Both body mass and thorax width declined non-linearly with age. Individuals appearing earlier in the flight period had significantly higher initial body mass and thorax width and their body mass declined faster than later ones. Initial body sizes of females were higher, but males' body sizes decreased slower. Initial thorax width showed higher annual variation than body mass. To our best knowledge, this is the first study that revealed phenotypic senescence in a natural butterfly population, using in vivo measurements. We found sexual differences in the rate of phenotypic senescence. Despite the annual variation of initial body sizes, the rate of senescence did not vary considerably across the years.

opencc-zeroDec 2014View details →

Data from: Correlation of shell phenotype and local environment suggests a role for natural selection in the evolution of Placostylus snails

The giant edible Placostylus snails of New Caledonia occur across a wide range of environmental conditions, from the dry southwest to the wetter central and northeastern regions. In large, slow-moving animals such as Placostylus, speciation could be assumed to be largely driven by allopatry and genetic drift as opposed to natural selection. We examined variation in shell morphology using geometric morphometrics and genetic structure within two species of Placostylus (P. fibratus, P. porphyrostomus), to determine the drivers of diversity in this group. Despite the current patchy distribution of snails on New Caledonia, both mtDNA and nuclear SNP data sets (>3000 loci) showed weak admixing between populations and species. Shell morphology was concordant with the genetic clusters we identified and had a strong relationship with local environment. The genetic data, in contrast to the morphological data, did not show concordance with climatic conditions, suggesting the snails are not limited in their ability to adapt to different environments. In sympatry, P. fibratus and P. porphyrostomus maintained genetic and morphological differences, suggesting a genetic basis of phenotypic variation. Convergence of shell shape was observed in two adjacent populations that are genetically isolated but experience similar habitat and climatic conditions. Conversely, some populations in contrasting environments were morphologically distinct although genetically indistinguishable. We infer that morphological divergence in the Placostylus snails of New Caledonia is mediated by adaptation to the local environment.

opencc-by-4.0Jul 2021View details →

Cosegmentation for Plant Phenotyping+ (CosegPP+) Data Repository Collected Via a High-Throughput Imaging System

CosegPP+ is an extension of CosegPP (https://doi.org/10.5281/zenodo.5117176) with binary masks for a collection of cosegmentation and segmentation algorithms.  We thank Vincent Stoeger for acquiring the dataset using LemnaTec at the University of Nebraska-Lincoln. If you use this dataset, please cite this paper: <table> <tbody> <tr></tr> <tr> <td> <div>Quiñones, R., Samal, A., Das Choudhury, S., & Muñoz-Arriola, F. (2023). OSC-CO2: coattention and cosegmentation framework for plant state change with multiple features. Frontiers in Plant Science, 14, 1211409.</div> </td> </tr> <tr> <td> </td> </tr> </tbody> </table>

opencc-zeroJul 2022View details →

Data from: Identification of candidate loci for adaptive phenotypic plasticity in natural populations of spadefoot toads

Phenotypic plasticity allows organisms to alter their phenotype in direct response to changes in the environment. Despite growing recognition of plasticity's role in ecology and evolution, few studies have probed plasticity's molecular bases—especially using natural populations. We investigated the genetic basis of phenotypic plasticity in natural populations of spadefoot toads (Spea multiplicata). Spea tadpoles normally develop into an 'omnivore' morph that is favored in long-lasting, low-density ponds. However, if tadpoles consume freshwater shrimp or other tadpoles, they can develop (via plasticity) into a 'carnivore' morph that is favored in shallow, high-density ponds. By combining natural variation in pond ecology and morph production with population genetic approaches, we identified candidate loci associated with morph (carnivores versus omnivores) and loci associated with adaptive phenotypic plasticity (adaptive versus maladaptive morph choice). Our candidate morph loci mapped to two genes, whereas our candidate plasticity loci mapped to 12 genes. In both cases, the identified genes tended to have functions related to their putative role in spadefoot tadpole biology. Our results thereby form the basis for future studies into the molecular mechanisms that mediate plasticity in spadefoots. More generally, these results illustrate how diverse loci might be deployed to mediate adaptive plasticity.