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opennotspecifiedMar 2013View details →

FIGURE 3 A–L in Phenotypic studies on terrestrial stigonematacean Cyanobacteria from the Atlantic Rainforest, São Paulo State, Brazil

FIGURE 3 A–L: Fischerella letestui. A: Detail of branching. B: Hormogonium. C: Initial stage of development. D–G: Details of the apices of branches. H–L: Branched main filaments. Scales: 10 µm in A (use for A, C–E, H–L) and B (use for B, F–G).

opennotspecifiedMar 2013View details →

FIGURE 1. A, B. A in Phenotypic studies on terrestrial stigonematacean Cyanobacteria from the Atlantic Rainforest, São Paulo State, Brazil

FIGURE 1. A, B. A. Map of South America; São Paulo State (SP) is indicated in Southeast Brazil. B. Map of São Paulo State; indication of the studied areas.

opennotspecifiedJun 2013View details →

FIGURE 2. A in Extension of the Cryptanthus range in Northeastern Brazil with new findings in the phenotypic variation including changes in the trichome's distribution, thus enhancing the understanding of the Cryptanthus zonatus complex (Bromeliaceae)

FIGURE 2. A. Two color morphs (maroon and green – indicated by the arrow) growing intermingled in the understory of Mata Estrela. B. Maroon color morph plant growing next to a banded individual that present a basal glabrous leaf (arrow) at Parque das Dunas. C. Signs of trichome loss on the older leaves (arrow), by a maroon banded individual from Parque das Dunas. D. Green individual showing dark red/maroon marks on the base of the leaves, Parque das Dunas. E. Two rosettes showing similar pigmentation (green along the center and dark red/maroon at the margins) but contrasting in the banded-lepidote versus glabrous adaxial surface. F. Individual displaying the colors green and wine-red spots (scale = 14 cm). G. Blooming individual of the banded form presenting a staminate flower. H. Bisexual flower of the maroon morph. I. Basal stolon (arrow), in the maroon morph. J. Basal stolon (arrow), in the banded morph.

opennotspecifiedJun 2013View details →

FIGURE 1 in Extension of the Cryptanthus range in Northeastern Brazil with new findings in the phenotypic variation including changes in the trichome's distribution, thus enhancing the understanding of the Cryptanthus zonatus complex (Bromeliaceae)

FIGURE 1. Map of Rio Grande do Norte state indicating the two new occurrences of Cryptanthus zonatus.

Condition-dependence of phenotypic integration and the evolvability of genitalic traits in a neriid fly

The spectacular diversity of insect male genitalia, and their relative insensitivity to the environment, have long puzzled evolutionary biologists and taxonomists. We asked whether the unusual evolvability of male genitalia could be associated with low morphological integration of genitalic traits, by comparison with male somatic traits and female traits. We also asked whether this pattern was robust to variation in resource availability during development, which affects adult condition. To address these questions, we manipulated larval diet quality in a split-brood design and compared levels of integration of male and female genitalic and somatic traits in the neriid fly, Telostylinus angusticollis. We found that male genitalic traits were substantially less integrated than male somatic traits, and less integrated than female genitalic traits. Female genitalic traits were also less integrated than female somatic traits, but the difference was less pronounced than in males. However, integration of male genitalic traits was negatively condition-dependent, with high-condition males exhibiting lower trait integration than low-condition males. Finally, genitalic traits exhibited lower larval diet family interactions than somatic traits. These results could help explain the unusually high evolvability of male genitalic traits in insects.

opencc-zeroDec 2021View details →

Isolation by geographical distance after release from Pleistocene refugia explains genetic and phenotypic variation in Xylotrupes siamensis (Coleoptera: Scarabaeidae)

Consistent and objective species delimitation is crucial to biodiversity studies, but challenges remain when conflicting taxonomic decisions have been made because different data sets and analytical methods were used to delineate species. In the rhinoceros beetle, Xylotrupes siamensis, the use of different morphological characters has resulted in taxonomic disagreement between studies. We used three molecular loci (mitochondrial CO1 and nuclear ITS2 and H3) to investigate the genetic divergence between populations exhibiting different male horn phenotypes. We also applied an approximate Bayesian computation approach to test alternative historical hypotheses that might explain the present genetic diversity among geographical populations. Furthermore, we used species distribution models to estimate the temporal variation in the geographical distribution of suitable habitats. The results show that the two phenotypic taxa within X. siamensis are not genetically structured and that their genetic structure can be explained using isolation by geographical distance. The emergence of the two phenotypic taxa might have been associated with historical isolation in separate refugia. However, spatial expansion and genetic interchange between populations might have gradually eroded the spatial genetic structure. We demonstrate that understanding the historical processes responsible for phenotypic divergence and genetic diversity among current populations could help with making evolutionarily coherent taxonomic decisions.

opencc-zeroDec 2015View details →

Data from: Unmanned aerial vehicles for high-throughput phenotyping and agronomic research

Advances in automation and data science have led agriculturists to seek real-time, high-quality, high-volume crop data to accelerate crop improvement through breeding and to optimize agronomic practices. Breeders have recently gained massive data-collection capability in genome sequencing of plants. Faster phenotypic trait data collection and analysis relative to genetic data leads to faster and better selections in crop improvement. Furthermore, faster and higher-resolution crop data collection leads to greater capability for scientists and growers to improve precision-agriculture practices on increasingly larger farms; e.g., site-specific application of water and nutrients. Unmanned aerial vehicles (UAVs) have recently gained traction as agricultural data collection systems. Using UAVs for agricultural remote sensing is an innovative technology that differs from traditional remote sensing in more ways than strictly higher-resolution images; it provides many new and unique possibilities, as well as new and unique challenges. Herein we report on processes and lessons learned from year 1—the summer 2015 and winter 2016 growing seasons–of a large multidisciplinary project evaluating UAV images across a range of breeding and agronomic research trials on a large research farm. Included are team and project planning, UAV and sensor selection and integration, and data collection and analysis workflow. The study involved many crops and both breeding plots and agronomic fields. The project's goal was to develop methods for UAVs to collect high-quality, high-volume crop data with fast turnaround time to field scientists. The project included five teams: Administration, Flight Operations, Sensors, Data Management, and Field Research. Four case studies involving multiple crops in breeding and agronomic applications add practical descriptive detail. Lessons learned include critical information on sensors, air vehicles, and configuration parameters for both. As the first and most comprehensive project of its kind to date, these lessons are particularly salient to researchers embarking on agricultural research with UAVs.

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 alternatively 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 14 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.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 alternatively 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 14 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.

Phenotypic variation in male Calopteryx splendens damselflies: The role of wing pigmentation and body size in thermoregulation

For an ectothermic insect, its color and size are important determinants of body temperature: dark colors absorb heat more efficiently, while larger bodies require more heat to reach a certain temperature. These dark colors are expressed using melanin, which has been intimately linked with an insect's thermoregulatory capabilities. Melanin is also linked with immune defense and is often used as a secondary sexual character in insects. There is a potential trade-off situation between thermoregulatory capabilities, immune defence and secondary sexual characters, all of which use melanin. Some Calopteryx damselflies, such as Calopteryx splendens, have melanin-based wing pigmentation that is sexually selected and drives intra- and interspecific territorial aggressions. Our goal was to experimentally study how the wing pigmentation and body size of C. splendens males affect their thermoregulation and especially their ability to become active after being cooled down. Our results are in line with our hypotheses showing that (i) individuals with larger wing spots had significantly faster activation times than those with smaller wing spots, and (ii) individuals with larger body size had significantly slower activation times than those with smaller body size. Both variables showed an interaction and thus are important in damselfly warm up and activation. We discuss the role wing pigmentation and thermoregulation can have on the behavioral patterns observed in Calopteryx species.

Olfactory Learning Supports an Adaptive Sugar-Aversion Gustatory Phenotype in the German Cockroach

An association of food sources with odors prominently guides foraging behavior in animals. To understand the interaction of olfactory memory and food preferences, we used glucose-averse (GA) German cockroaches. Multiple populations of cockroaches evolved a gustatory polymor-phism where glucose is perceived as a deterrent and enables GA cockroaches to avoid eating glucose-containing toxic baits. Comparative behavioral analysis using an operant conditioning paradigm revealed that learning and memory guide foraging decisions. Cockroaches learned to associate specific food odors with fructose (phagostimulant, reward) within only 1 hr of condi-tioning session, and with caffeine (deterrent, punishment) after only three 1 hr conditioning ses-sions. Glucose acted as reward in wild type (WT) cockroaches, but GA cockroaches learned to avoid an innately attractive odor that was associated with glucose. Olfactory memory was retained for at least 3 days after three 1 hr conditioning sessions. Our results reveal that specific tastants can serve as potent reward or punishment in olfactory associative learning, which reinforces gustatory food preferences. Olfactory learning therefore reinforces behavioral resistance of GA cockroaches to sugar-containing toxic baits. Cockroaches may also generalize their olfactory learning to baits that contain the same or similar attractive odors even if they do not contain glucose.

opencc-by-4.0Jul 2021View details →

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

CosegPP is a data repository that contains four datasets for plant phenotyping. Each dataset contains:  <ol> <li>two species physically different for challenging segmentation. Buckwheat is a thin plant with a variety sizes of leaves and Sunflower is a bushy plant that contains flowering;</li> <li>the most commonly used induced environments in plant phenotyping such as a control and drought-induced; </li> <li>a temporal resolution that begins with the plants vegetative stage and ends with the plant fully matured;</li> <li>modalities (infrared, visible, near infrared) that are commonly used in plant phenotyping analysis; and </li> <li>multiple perspectives that are becoming widely acquired in plant phenotyping analysis due to its potential for three dimensional analysis.</li> </ol> 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: Quiñones R, Munoz-Arriola F, Choudhury SD, Samal A (2021) Multi-feature data repository development and analytics for image cosegmentation in high-throughput plant phenotyping. PLoS ONE 16(9): e0257001. <a href="https://doi.org/10.1371/journal.pone.0257001">https://doi.org/10.1371/journal.pone.0257001</a>

opennotspecifiedJul 2021View details →

FIGURE 1 in Phenotypic variation in Heremites vittatus (Olivier, 1804) (Sauria: Scincidae) from Iran and Turkey

FIGURE 1. Sampling localities of all examined specimens from Iran and Turkey. Colors refer to the country specimens (Red refer to Turkish specimens; Blue refer to Iranian specimens). Numbers next to the dots refer to the specimens in Appendix 1.

opennotspecifiedJul 2021View details →

FIGURE 3 in Phenotypic variation in Heremites vittatus (Olivier, 1804) (Sauria: Scincidae) from Iran and Turkey

FIGURE 3. Ordination of the individuals of all localities on the first two canonical variates of 16 characters.

opennotspecifiedJul 2021View details →

FIGURE 2 in Phenotypic variation in Heremites vittatus (Olivier, 1804) (Sauria: Scincidae) from Iran and Turkey

FIGURE 2. Ordination of the individuals of all localities on the first two principal components of 16 characters.

Associations among cotyledon developmental stability, canalization and phenotypic plasticity in response to shading and burial depth in five herbaceous species at early seedling stage

Premise of research. Cotyledons have important functions in early seedling stage and have important effects on later stages, but we know little about the relationships among developmental stability, canalization and phenotypic plasticity in cotyledons. Methodology. We conducted a field experiment with five herbaceous species, by subjecting them to contrasting light conditions and burial depths and measuring their cotyledon size and fluctuating asymmetry (random deviation from perfect bilateral symmetry, indicating developmental stability or instability), coefficient of variation and plasticity of cotyledon size, to investigate the relationships among cotyledon developmental stability, canalization and plasticity in response to shading and deep burial. Pivotal results. Pharbitis purpurea, Convolvulus arvensis and Carpesium abrotanoides had increased cotyledon size in response to shading at both burial depths; Abutilon theophrasti showed reduced cotyledon size in response to shading vs. full light at shallow depth, but greater cotyledon size in response to both shading and deep burial. Shading increased cotyledon fluctuating asymmetry of P. purpurea and C. abrotanoides, while deep burial decreased it. Cotyledon fluctuating asymmetry had positive correlations with coefficient of variation and plasticity in response to shade in shading, with little correlation between coefficient of variation and plasticity. Conclusions. Results suggested A. theophrasti may have greater tolerance for multiple stresses than the other species, and deep burial may improve shade tolerance of cotyledons through moderate level of stress selection. Both developmental instability and decreased canalization may indicate the state of faster growth. Developmental instability can facilitate more-active response to shading in cotyledon, while the relationship between canalization and plasticity should be more complex.

Associations between leaf developmental stability, variability, canalization and phenotypic plasticity in Abutilon theophrasti

Developmental stability, canalization, and phenotypic plasticity are the most common sources of phenotypic variation, yet comparative studies investigating the relationships between these sources, specifically in plants, are lacking. To investigate the relationships among developmental stability or instability, developmental variability, canalization and plasticity in plants, we conducted a field experiment with Abutilon theophrasti, by subjecting plants to three densities under infertile vs. fertile soil conditions. We measured the leaf width (leaf size) and calculated fluctuating asymmetry (FA), coefficient of variation within and among individuals (CVintra and CVinter), and plasticity (PIrel) in leaf size at day 30, 50 and 70 of plant growth, to analyze the correlations among these variables in response to density and soil conditions, at each of or across all growth stages. Results showed increased density led to lower leaf FA, CVintra and PIrel and higher CVinter in fertile soil. A positive correlation between FA and PIrel occurred in infertile soil, while correlations between CVinter and PIrel and between CVinter and CVintra were negative at high density and/or in fertile soil, with non-significant correlations among them in other cases. Results suggested the complexity of responses of developmental instability, variability and canalization in leaf size as well as their relationships, which depend on the strength of stresses. Intense aboveground competition that accelerates the decrease in leaf size (leading to lower plasticity) will be more likely to reduce developmental instability, variability and canalization in leaf size. Increased developmental instability and intra- and inter-individual variability should be advantageous and facilitate adaptive plasticity in less stressful conditions, thus they are more likely to positively correlate with plasticity; whereas developmental stability and canalization with lower developmental variability should be beneficial for stabilizing plant performance in more stressful conditions, where they tend to have more negative correlations with plasticity.

opennotspecifiedJun 2014View details →

FIGURE 2 in Nodularia (Cyanobacteria, Nostocaceae): a phylogenetically uniform genus with variable phenotypes

FIGURE 2. Micrographs of selected strains from the individual subclusters in the phylogenetic tree (Fig. 1). A. Nodularia sp. Saline 2, subcluster I. B. Nodularia sp. strain Saline 2, subcluster I. C. Nodularia sphaerocarpa HBU25, subcluster I. D. Nodularia moravica CCALA 797 with two types of trichome morphology, subcluster II. E. Nodularia armorica L7, subcluster II. F. Nodularia sphaerocarpa HBU22, subcluster III. G. Nodularia harveyana BOB1, subcluster III. H. Nodularia harveyana SAG 44.85, subcluster IV I. Nodularia cf. harveyana HBU26, outside the subclusters. Akinetes are indicated by an asterisk, and heterocytes are indicated by an arrow Scale bar = 10 μm.

opennotspecifiedJun 2014View details →

FIGURE 1 in Nodularia (Cyanobacteria, Nostocaceae): a phylogenetically uniform genus with variable phenotypes

FIGURE 1. Bayesian inference (BI) phylogenetic tree inferred from a 79 × 1917 nucleotide alignment (partial 16S rDNA+rbcLX) representing the current GenBank data on heterocytous cyanobacteria and focusing on the genus Nodularia. Branch supports (percent posterior probablity of BI branches, 1000 pseudoreplications for maximum likelihood [ML] and maximum parsimony [MP]) ≥ 50% are provided in the following form: BI/ML/MP. Nodes with 100% support from all methods are marked with an asterisk. In the tree, strains of the genus Nodularia formed a monophyletic cluster, within which four subclusters (I–IV) could be distinguished (as described in the text).

Widespread coexistence of self-compatible and self-incompatible phenotypes in a diallelic self-incompatibility system in Ligustrum vulgare (Oleaceae)

The breakdown of self-incompatibility (SI) in angiosperms is one of the most commonly observed evolutionary transitions. While multiple examples of SI breakdown have been documented in natural populations, there is strikingly little evidence of stable within-population polymorphism with both inbreeding (self-compatible) and outcrossing (self-incompatible) individuals. This absence of breeding system polymorphism corroborates theoretical expectations that predict that in/outbreeding polymorphism is possible only under very restricted conditions. However, theory also predicts that a diallelic sporophytic SI system should facilitate the maintenance of such polymorphism. We tested this prediction by studying the breeding system of Ligustrum vulgare L., an insect pollinated hermaphroditic species of the Oleaceae family. Using stigma tests with controlled pollination and paternity assignment of open-pollinated progenies, we confirmed the existence of two self-incompatibility groups in this species. We also demonstrated the occurrence of self-compatible individuals in different populations of Western Europe arising from a mutation affecting the functioning of the pollen component of SI. Our results show that the observed low frequency of self-compatible individuals in natural populations is compatible with theoretical predictions only if inbreeding depression is very high.