Foraging predicts the evolution of warning coloration and mimicry in snakes

Warning coloration and Batesian mimicry are classic examples of Darwinian evolution, but empirical evolutionary patterns are often paradoxical. We test whether foraging costs predict the evolution of striking coloration by integrating genetic and ecological data for aposematic and mimetic snakes (Elapidae and Dipsadidae). Our phylogenetic comparison on a total of 432 species demonstrated that dramatic changes in coloration were well predicted by foraging strategy. Multiple tests consistently indicated that warning coloration and conspicuous mimicry were more likely to evolve in species where foraging costs of conspicuous appearance were relaxed by poor vision of their prey, concealed habitat, or nocturnal activity. Reversion to crypsis was also well predicted by ecology for elapids but not for dipsadids. In contrast to a theoretical prediction and general trends, snakes' conspicuous coloration was correlated with secretive ecology, suggesting that a selection regime underlies evolutionary patterns. We also found evidence that mimicry of inconspicuous models (pitvipers) may have evolved in association with foraging demand for crypsis. These findings demonstrate that foraging is an important factor necessary to understand the evolution, persistence, and diversity of warning coloration and mimicry of snakes, highlighting the significance of additional selective factors in solving the warning coloration paradox.

Natural uORF variation in plants

Taking advantage of natural variation promotes our understanding of phenotypic diversity and trait evolution, ultimately accelerating plant breeding, in which the identification of causal variations is critical. To date, sequence variations in the coding region and transcription level polymorphisms caused by variations in the promoter have been prioritized. An upstream open reading frame (uORF) in the 5' untranslated region (5' UTR) regulates gene expression at the post-transcription or translation level. In recent years, studies have demonstrated that natural uORF variations shape phenotypic diversity. This opinion article highlights recent researches and speculates on future directions for natural uORF variation in plants.

Does size-selective harvesting erode adaptive potential to thermal stress?

Overharvesting is a serious threat to many fish populations. High mortality and directional selection on body size can cause evolutionary change in exploited populations via selection for a specific phenotype and a potential reduction in phenotypic diversity. Whether the loss of phenotypic diversity that accompanies directional selection impairs response to environmental stress is not known. To address this question, we exposed three zebrafish selection lines to thermal stress. Two lines had experienced directional selection for (1) large and (2) small body size, and one was (3) subject to random removal of individuals with respect to body size (i.e. line with no directional selection). Selection lines were exposed to three temperatures (elevated, 34°C; ambient, 28°C; low, 22°C) to determine the response to an environmental stressor (thermal stress). We assessed differences among selection lines in their life history (growth and reproduction), physiological traits (metabolic rate and critical thermal max) and behaviour (activity and feeding behaviour) when reared at different temperatures. Lines experiencing directional selection (i.e. size selected) showed reduced growth rate and a shift in average phenotype in response to lower or elevated thermal stress compared with fish from the random-selected line. Our data indicate that populations exposed to directional selection can have a more limited capacity to respond to thermal stress compared with fish that experience a comparable reduction in population size (but without directional selection). Future studies should aim to understand the impacts of environmental stressors on natural fish stocks.

Phenotypic and Genotypic Variation of Cultivated Panax quinquefolius

American ginseng (Panax quinquefolius) is widely used due to its medicinal properties. Ontario is a major producer of cultivated American ginseng, where seeds were originally collected from the wild without any subsequent scientific selection, and thus the crop is potentially very diverse. A collection of 162 American ginseng plants was harvested from a small area in a commercial garden and phenotyped for morphological traits, such as root grade, stem length, and fresh and dry weights of roots, leaves, stems, and seeds. All of the traits showed a range of values, and correlations were observed between root and stem weights, root dry weight and leaf dry weight, as well as root and leaf fresh weights. The plants were also genotyped using single nucleotide polymorphisms (SNPs) at the PW16 locus. SNP analysis revealed 22 groups based on sequence relatedness with some groups showing no SNPs and others being more diverse. The SNP groups correlated with significant differences in some traits, such as stem length and leaf weight. This study provides insights into the genetic and phenotypic diversity of cultivated American ginseng grown under similar environmental conditions, and the relationship between different phenotypes, as well as genotype and phenotype, will aid in future selection programs to develop American ginseng cultivars with desirable agronomic traits.

Phenotypic and genetic characterization of an Avena sativa L. germplasm collection of diverse origin: implications for food-oat breeding in Chile

Oats are known for their nutritional value and also for their beneficial properties on human health, such as the reduction of cholesterol levels and risk of coronary heart disease; they are an important export product for Chile. During the last decade (2010-2022) over 90% of the oat cultivated area in Chile has been covered with Avena sativa L. cv. Supernova INIA. This lack of genetic diversity in a context of climate change could limit the long-term possibility of growing oats in Chile. The present study is a phenotypic and genetic analysis of 132 oat cultivars and pure lines of diverse origin that can be considered as potential breeding material. The germplasm was evaluated for 28 traits and analyzed with 14 SSR markers. The effects of genotypes on phenotype were significant over all traits (P ≤ 0.05). Most traits exhibited moderate to high broad-sense heritability with exceptions such as yield (H2 = 0.27) and hulls staining (H2 = 0.32). Significant undesirable correlations between traits were generally of small biological importance, which is auspicious for achieving breeding objectives. Some of the heritability data and correlations provided here have not been previously reported. The overall phenotypic diversity was high (H' = 0.68 ± 0.18). The germplasm was grouped into three phenotypic clusters, differing in their qualities for breeding. Twenty-six genotypes outperforming Supernova INIA were identified for breeding of conventional food-oats. The genetic diversity of the germplasm was moderate on average (He = 0.58 ± 0.03), varying between 0.32 (AM22) and 0.77 (AME178). Two genetic subpopulations supported by the Structure algorithm exhibited a genetic distance of 0.24, showing low divergence of the germplasm. The diversity and phenotypic values found in this collection of oat genotypes are promising with respect to obtaining genetic gain in the short term in breeding programs. However, the similar genetic diversity, higher phenotypic diversity, and better phenotypic performance of the germplasm created in Chile compared to foreign germplasm suggest that germplasm harboring new genetic diversity will be key to favor yield and quality in new oat cultivars in the long term.

Developing a novel selection method for alcoholic fermentation starters by exploring wine yeast microbiota from Greece

The selection of native yeast for alcoholic fermentation in wine focuses on ensuring the success of the process and promoting the quality of the final product. The purpose of this study was firstly to create a large collection of new yeast isolates and categorize them based on their oenological potential. Additionally, the geographical distribution of the most dominant species, Saccharomyces cerevisiae, was further explored. Towards this direction, fourteen spontaneously fermented wines from different regions of Greece were collected for yeast typing. The yeast isolates were subjected in molecular analyses and identification at species level. RAPD (Random Amplified Polymorphic DNA) genomic fingerprinting with the oligo-nucleotide primer M13 was used, combined with Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) technique. All yeast isolates were scrutinized for their sensitivity to killer toxin, production of non-desirable metabolites such as acetic acid and H2S, β-glucosidase production and resistance to the antimicrobial agent; SO2. In parallel, S. cerevisiae isolates were typed at strain level by interdelta - PCR genomic fingerprinting. S. cerevisiae strains were examined for their fermentative capacity in laboratory scale fermentation on pasteurized grape must. Glucose and fructose consumption was monitored daily and at the final point a free sorting task was conducted to categorize the samples according to their organoleptic profile. According to our results, among the 190 isolates, S. cerevisiae was the most dominant species while some less common non-Saccharomyces species such as Trigonopsis californica, Priceomyces carsonii, Zygosaccharomyces bailii, Brettanomyces bruxellensis and Pichia manshurica were identified in minor abundancies. According to phenotypic typing, most isolates were neutral to killer toxin test and exhibited low acetic acid production. Hierarchical Cluster Analysis revealed the presence of four yeast groups based on phenotypic fingerprinting. Strain level typing reported 20 different S. cerevisiae strains from which 65% indicated fermentative capacity and led to dry wines. Sensory evaluation results clearly discriminated the produced wines and consequently, the proposed yeast categorization was confirmed. A novel approach that employs biostatistical tools for a rapid screening and classification of indigenous wine yeasts with oenological potential, allowing a more efficient preliminary selection or rejection of isolates is proposed.

Phenotypic Diversity of a Leafroller Archips podana (Lepidoptera, Tortricidae) Does Not Change along an Industrial Pollution Gradient

Morphological polymorphism offers rich opportunities for studying the eco-evolutionary mechanisms that drive the adaptations of local populations to heterogeneous and changing environments. In this study, I explore the association between pollution load, abundance of large fruit-tree tortrix Archips podana and its within-species diversity (expressed in the presence of apical and/or lateral prongs on the phallus in male genitalia) across 26 study sites located 0.5 to 31 km from the industrial city of Lipetsk in central Russia. The Shannon diversity index, calculated from the frequencies of four morphs, correlated neither with the distance to the nearest industrial polluter (a proxy of pollution load) nor with the number of moths captured by pheromone traps (a measure of population abundance). The statistical power of the correlation analysis was sufficient (67%) to detect a medium effect (i.e., Pearson correlation coefficient with an absolute value of 0.40), if it existed. I conclude that the four phenotypes of A. podana do not differ in tolerance to industrial pollution and similarly respond to pollution-induced environmental disturbance. This is the first study of industrial pollution impacts on within-species diversity of insects expressed in the discrete traits of their male genitalia.

[Comprehensive evaluation of Pinellia ternata germplasm resources based on phenotypic trait classification]

The evaluation of germplasm resources is the prerequisite for the development, utilization, and conservation of Chinese medicinal resources. The selection of excellent germplasm is the key to the breeding and orderly production of Pinellia ternata. In this study, 21 germplasm materials of P. ternata from major production areas in China were collected and analyzed for population diversity after phenotypic preliminary screening. The results have revealed that the P. ternata population has abundant phenotypic variation, and the phenotypic changes could be divided into five phenotypes in terms of organ trait variation. Further analysis of variation in 20 quantitative traits of the population revealed that the coefficient of variation for adenosine content(339.05%) was the largest, while the coefficient of variation for the underground plant height(16.35%) was the smallest. Correlation analysis showed that there was a strong correlation among various traits, with 52 pairs of traits showing highly significant correlation(P<0.01) and 19 pairs of traits showing a significant correlation(P<0.05). The 21 germplasms in the test could be classified into three major clusters by cluster analysis, with Cluster Ⅱ having the highest number and content of nucleosides, making it suitable for the selection and breeding of P. ternata varieties with high content of nucleosides. The yield in Cluster Ⅲ was higher than that in other groups, making it suitable for the selection and breeding of P. ternata varieties with a high yield. All trait indicators could be simplified into five principal component factors through principal component analysis, and the cumulative contribution rate was up to 86.04%. Further, comprehensive analysis using membership function and stepwise regression analysis identified nine traits, such as plant height, main leaf length, and underground plant height as characteristic indicators for the comprehensive evaluation of germplasm resources of P. ternata. BX007, BX008, and BX005 were identified as germplasms with both high yield and high uridine content, with BX007 having the highest uridine content of 479.51 μg·g~(-1). It belonged to the germplasm of P. ternata with double bulbils and could be cultivated as a potential good variety. Based on the phenotypic classification of P. ternata, systematic resource evaluation was carried out in this study, which could lay a foundation for the excavation of genetic resources and the breeding of new varieties of P. ternata.

Cranial morphology of Balkan and West Asian livestock guardian dogs

Several large "shepherd" or livestock guardian dog (LGD) breeds were historically selectively bred to protect sheep and goat flocks in the Balkans, Anatolia, and the Caucasus regions. Although these breeds exhibit similar behavior, their morphology is different. Yet, the fine characterization of the phenotypic differences remains to be analyzed. The aim of this study is to characterize cranial morphology in the specific Balkan and West Asian LGD breeds. We use a 3D geometric morphometric in order to assess morphological differences regarding both shape and size between LGD breeds and compare this phenotypic diversity to close relative wild canids. Our results indicate that Balkan and Anatolian LGDs form a distinct cluster within a relatively large dog cranial size and shape diversity. Most LGDs display a cranial morphology that could be described as intermediate to the mastiff breeds and large herding dogs, except for the Romanian Mioritic shepherd which has a more brachycephalic cranium strongly resembling the bully-type dog cranial morphotype. Although often considered to represent an ancient type of dog, the Balkan-West Asian LGDs are clearly distinguishable from wolves, dingoes, and most other primitive and spitz-type dogs and this group displays a surprising cranial diversity.

Unraveling the enigma of tumor-associated macrophages: challenges, innovations, and the path to therapeutic breakthroughs

Tumor-associated macrophages (TAMs) are integral to the tumor microenvironment (TME), influencing cancer progression significantly. Attracted by cancer cell signals, TAMs exhibit unparalleled adaptability, aligning with the dynamic tumor milieu. Their roles span from promoting tumor growth and angiogenesis to modulating metastasis. While substantial research has explored the fundamentals of TAMs, comprehending their adaptive behavior, and leveraging it for novel treatments remains challenging. This review delves into TAM polarization, metabolic shifts, and the complex orchestration of cytokines and chemokines determining their functions. We highlight the complexities of TAM-targeted research focusing on their adaptability and potential variability in therapeutic outcomes. Moreover, we discuss the synergy of integrating TAM-focused strategies with established cancer treatments, such as chemotherapy, and immunotherapy. Emphasis is laid on pioneering methods like TAM reprogramming for cancer immunotherapy and the adoption of single-cell technologies for precision intervention. This synthesis seeks to shed light on TAMs' multifaceted roles in cancer, pinpointing prospective pathways for transformative research and enhancing therapeutic modalities in oncology.

The Microevolution of Antifungal Drug Resistance in Pathogenic Fungi

The mortality rates of invasive fungal infections remain high because of the limited number of antifungal drugs available and antifungal drug resistance, which can rapidly evolve during treatment. Mutations in key resistance genes such as ERG11 were postulated to be the predominant cause of antifungal drug resistance in the clinic. However, recent advances in whole genome sequencing have revealed that there are multiple mechanisms leading to the microevolution of resistance. In many fungal species, resistance can emerge through ERG11-independent mechanisms and through the accumulation of mutations in many genes to generate a polygenic resistance phenotype. In addition, genome sequencing has revealed that full or partial aneuploidy commonly occurs in clinical or microevolved in vitro isolates to confer antifungal resistance. This review will provide an overview of the mutations known to be selected during the adaptive microevolution of antifungal drug resistance and focus on how recent advances in genome sequencing technology have enhanced our understanding of this process.

Study on the Phenotypic Diversity of 33 Ornamental Xanthoceras sorbifolium Cultivars

Xanthoceras sorbifolium, belonging to the family Sapindaceae, has a beautiful tree shape, elegant leaves, large and many brightly colored flowers, and a long flowering duration. This plant is widely applied in gardens. In this study, 33 cultivars of Xanthoceras sorbifolium were selected from the perspective of ornamental properties, and their phenotypic traits, such as leaves, flowers, and branches, were measured and analyzed, and their phenotypic diversity was comprehensively evaluated using principal component analysis, in order to investigate the phenotypic diversity characteristics of Xanthoceras sorbifolium. The results showed that the genetic diversity index of the qualitative traits varied from 0.14 to 1.50, and that of quantitative traits varied from 1.76 to 2.05. The quantitative traits were more diverse than the qualitative traits. The coefficient of variation of the qualitative traits ranged from 16.90% to 57.96%, and that of quantitative traits ranged from 12.92% to 32.87%. The phenotypic traits of the tested cultivars had relatively rich variation. Furthermore, the level of the phenotypic diversity index of Xanthoceras sorbifolium was not consistent with the level of coefficient of variation, indicating large variation and uneven distribution of variation. Through principal component analysis, 17 quantitative characters were extracted into five principal components, with a cumulative contribution rate of 79.82%, representing the primary information on the quantitative characters of ornamental Xanthoceras sorbifolium cultivars. The F value of the 33 samples ranged from -2.79 to 1.93, and the comprehensive scores of seven cultivars were greater than 1, indicating that these cultivars had rich phenotypic diversity. Therefore, the screening, development, and utilization of fine germplasm resources of Xanthoceras sorbifolium should focus on these cultivars. The 33 cultivars were subsequently clustered into five categories through systematic clustering. The cluster analysis provided references for breeding ornamental Xanthoceras sorbifolium cultivars with different utilization values, such as large white flowers, small red flowers, large red flowers, large orange flowers, and double-petaled flowers.

Are Appearances Deceiving? Morpho-Genetic Complexity of the Eumerus tricolor Group (Diptera: Syrphidae) in Europe, with a Focus on the Iberian Peninsula

Eumerus Meigen, 1822 is one of the largest Syrphidae genera in the Palaearctic Region, with the highest levels of taxonomic diversity found in the Eumerus tricolor species group. Despite its high diversity, the interspecific levels of morphological variability can be low. Additionally, some species may show certain levels of intraspecific variability. Hence, species delimitation may become challenging. In this work, we assessed the diversity of the E. tricolor group in the Iberian Peninsula through an integrative analysis of nomenclature, morphology and the 5' (COI-5') and 3' (COI-3') end regions of the Cytochrome c oxidase subunit I gene. Two new species, Eumerus ancylostylus Aguado-Aranda & Ricarte sp. n. and Eumerus petrarum Aguado-Aranda, Nedeljković & Ricarte sp. n., were described, and their intra- and interspecific variations discussed. In addition, the first barcodes of Iberian members of the E. tricolor group were obtained, and the distribution ranges of all species were mapped within the study area. The systematic position of the new species is discussed based on the resulting COI-based trees. The male genitalia of Eumerus hispanicus van der Goot, 1966 and Eumerus bayardi Séguy, 1961 were studied and illustrated. A lectotype was designated for Eumerus lateralis (Zetterstedt, 1819). An updated dichotomous key for all known European species of the E. tricolor group is provided. The egg of E. petrarum sp. n. is also described.

A shark-inspired general model of tooth morphogenesis unveils developmental asymmetries in phenotype transitions

Developmental complexity stemming from the dynamic interplay between genetic and biomechanic factors canalizes the ways genotypes and phenotypes can change in evolution. As a paradigmatic system, we explore how changes in developmental factors generate typical tooth shape transitions. Since tooth development has mainly been researched in mammals, we contribute to a more general understanding by studying the development of tooth diversity in sharks. To this end, we build a general, but realistic, mathematical model of odontogenesis. We show that it reproduces key shark-specific features of tooth development as well as real tooth shape variation in small-spotted catsharks Scyliorhinus canicula. We validate our model by comparison with experiments in vivo. Strikingly, we observe that developmental transitions between tooth shapes tend to be highly degenerate, even for complex phenotypes. We also discover that the sets of developmental parameters involved in tooth shape transitions tend to depend asymmetrically on the direction of that transition. Together, our findings provide a valuable base for furthering our understanding of how developmental changes can lead to both adaptive phenotypic change and trait convergence in complex, phenotypically highly diverse, structures.

Contrasting transcriptomic patterns reveal a genomic basis for drought resilience in the relict fir Abies pinsapo Boiss

Climate change challenges the adaptive capacity of several forest tree species in the face of increasing drought and rising temperatures. Therefore, understanding the mechanistic connections between genetic diversity and drought resilience is highly valuable for conserving drought-sensitive forests. Nonetheless, the post-drought recovery in trees from a transcriptomic perspective has not yet been studied by comparing contrasting phenotypes. Here, experimental drought treatments, gas-exchange dynamics and transcriptomic analysis (RNA-seq) were performed in the relict and drought-sensitive fir Abies pinsapo Boiss. to identify gene expression differences over immediate (24 h) and extended drought (20 days). Post-drought responses were investigated to define resilient and sensitive phenotypes. Single nucleotide polymorphisms (SNPs) were also studied to characterize the genomic basis of A. pinsapo drought resilience. Weighted gene co-expression network analysis showed an activation of stomatal closing and an inhibition of plant growth-related genes during the immediate drought, consistent with an isohydric dynamic. During the extended drought, transcription factors, as well as cellular damage and homeostasis protection-related genes prevailed. Resilient individuals activate photosynthesis-related genes and inhibit aerial growth-related genes, suggesting a shifting shoot/root biomass allocation to improve water uptake and whole-plant carbon balance. About, 152 fixed SNPs were found between resilient and sensitive seedlings, which were mostly located in RNA-activity-related genes, including epigenetic regulation. Contrasting gene expression and SNPs were found between different post-drought resilience phenotypes for the first time in a forest tree, suggesting a transcriptomic and genomic basis for drought resilience. The obtained drought-related transcriptomic profile and drought-resilience candidate genes may guide conservation programs for this threatened tree species.

Evaluation of a Sugarcane (Saccharum spp.) Hybrid F1 Population Phenotypic Diversity and Construction of a Rapid Sucrose Yield Estimation Model for Breeding

Sugarcane is the major sugar-producing crop worldwide, and hybrid F₁ populations are the primary populations used in breeding. Challenged by the sugarcane genome's complexity and the sucrose yield's quantitative nature, phenotypic selection is still the most commonly used approach for high-sucrose yield sugarcane breeding. In this study, a hybrid F₁ population containing 135 hybrids was constructed and evaluated for 11 traits (sucrose yield (SY) and its related traits) in a randomized complete-block design during two consecutive growing seasons. The results revealed that all the traits exhibited distinct variation, with the coefficient of variation (CV) ranging from 0.09 to 0.35, the Shannon-Wiener diversity index (H') ranging between 2.64 and 2.98, and the broad-sense heritability ranging from 0.75 to 0.84. Correlation analysis revealed complex correlations between the traits, with 30 trait pairs being significantly correlated. Eight traits, including stalk number (SN), stalk diameter (SD), internode length (IL), stalk height (SH), stalk weight (SW), Brix (B), sucrose content (SC), and yield (Y), were significantly positively correlated with sucrose yield (SY). Cluster analysis based on the 11 traits divided the 135 F₁ hybrids into three groups, with 55 hybrids in Group I, 69 hybrids in Group II, and 11 hybrids in Group III. The principal component analysis indicated that the values of the first four major components' vectors were greater than 1 and the cumulative contribution rate reached 80.93%. Based on the main component values of all samples, 24 F₁ genotypes had greater values than the high-yielding parent 'ROC22' and were selected for the next breeding stage. A rapid sucrose yield estimation equation was established using four easily measured sucrose yield-related traits through multivariable linear stepwise regression. The model was subsequently confirmed using 26 sugarcane cultivars and 24 F₁ hybrids. This study concludes that the sugarcane F₁ population holds great genetic diversity in sucrose yield-related traits. The sucrose yield estimation model, ySY=2.01xSN+8.32xSD+0.79xB+3.44xSH-47.64, can aid to breed sugarcane varieties with high sucrose yield.

De novo transcriptome sequencing and gene co-expression reveal a genomic basis for drought sensitivity and evidence of a rapid local adaptation on Atlas cedar (Cedrus atlantica)

Introduction

Understanding the adaptive capacity to current climate change of drought-sensitive tree species is mandatory, given their limited prospect of migration and adaptation as long-lived, sessile organisms. Knowledge about the molecular and eco-physiological mechanisms that control drought resilience is thus key, since water shortage appears as one of the main abiotic factors threatening forests ecosystems. However, our current background is scarce, especially in conifers, due to their huge and complex genomes.

Methods

Here we investigated the eco-physiological and transcriptomic basis of drought response of the climate change-threatened conifer Cedrus atlantica. We studied C. atlantica seedlings from two locations with contrasting drought conditions to investigate a local adaptation. Seedlings were subjected to experimental drought conditions, and were monitored at immediate (24 hours) and extended (20 days) times. In addition, post-drought recovery was investigated, depicting two contrasting responses in both locations (drought resilient and non-resilient). Single nucleotide polymorphisms (SNPs) were also studied to characterize the genomic basis of drought resilience and investigate a rapid local adaptation of C. atlantica.

Results

De novo transcriptome assembly was performed for the first time in this species, providing differences in gene expression between the immediate and extended treatments, as well as among the post-drought recovery phenotypes. Weighted gene co-expression network analysis showed a regulation of stomatal closing and photosynthetic activity during the immediate drought, consistent with an isohydric dynamic. During the extended drought, growth and flavonoid biosynthesis inhibition mechanisms prevailed, probably to increase root-to-shoot ratio and to limit the energy-intensive biosynthesis of secondary metabolites. Drought sensitive individuals failed in metabolism and photosynthesis regulation under drought stress, and in limiting secondary metabolite production. Moreover, genomic differences (SNPs) were found between drought resilient and sensitive seedlings, and between the two studied locations, which were mostly related to transposable elements.

Discussion

This work provides novel insights into the transcriptomic basis of drought response of C. atlantica, a set of candidate genes mechanistically involved in its drought sensitivity and evidence of a rapid local adaptation. Our results may help guide conservation programs for this threatened conifer, contribute to advance drought-resilience research and shed light on trees' adaptive potential to current climate change.

Modeling the Evolution of Rates of Continuous Trait Evolution

Rates of phenotypic evolution vary markedly across the tree of life, from the accelerated evolution apparent in adaptive radiations to the remarkable evolutionary stasis exhibited by so-called "living fossils". Such rate variation has important consequences for large-scale evolutionary dynamics, generating vast disparities in phenotypic diversity across space, time, and taxa. Despite this, most methods for estimating trait evolution rates assume rates vary deterministically with respect to some variable of interest or change infrequently during a clade's history. These assumptions may cause underfitting of trait evolution models and mislead hypothesis testing. Here, we develop a new trait evolution model that allows rates to vary gradually and stochastically across a clade. Further, we extend this model to accommodate generally decreasing or increasing rates over time, allowing for flexible modeling of "early/late bursts" of trait evolution. We implement a Bayesian method, termed "evolving rates" (evorates for short), to efficiently fit this model to comparative data. Through simulation, we demonstrate that evorates can reliably infer both how and in which lineages trait evolution rates varied during a clade's history. We apply this method to body size evolution in cetaceans, recovering substantial support for an overall slowdown in body size evolution over time with recent bursts among some oceanic dolphins and relative stasis among beaked whales of the genus Mesoplodon. These results unify and expand on previous research, demonstrating the empirical utility of evorates.

Microglia in Circumventricular Organs: The Pineal Gland Example

The circumventricular organs (CVOs) are unique areas within the central nervous system. They serve as a portal for the rest of the body and, as such, lack a blood-brain barrier. Microglia are the primary resident immune cells of the brain parenchyma. Within the CVOs, microglial cells find themselves continuously challenged and stimulated by local and systemic stimuli, even under steady-state conditions. Therefore, CVO microglia in their typical state often resemble the activated microglial forms found elsewhere in the brain as they are responding to pathological conditions or other stressors. In this review, I focus on the dynamics of CVO microglia, using the pineal gland as a specific CVO example. Data related to microglia heterogeneity in both homeostatic and unhealthy environments are presented and discussed, including those recently generated by using advanced single-cell and single-nucleus technology. Finally, perspectives in the CVO microglia field are also included.Summary StatementMicroglia in circumventricular organs (CVOs) continuously adapt to react differentially to the diverse challenges they face. Herein, I discuss microglia heterogeneity in CVOs, including pineal gland. Further studies are needed to better understand microglia dynamics in these unique brain areas. .

Genomic and phenotypic biology of a novel Dickeya zeae WH1 isolated from rice in China: Insights into pathogenicity and virulence factors

Soft rot caused by Dickeya zeae is an important bacterial disease affecting rice and other plants worldwide. In this study, Nanopore and Illumina sequencing platforms were used to sequence the high-quality complete genome of a novel D. zeae strain WH1 (size: 4.68 Mb; depth: 322.37x for Nanopore, 243.51x for Illumina; GC content: 53.59%), which was isolated from healthy rice root surface together with Paenibacillus polymyxa, a potential biocontrol bacterium against D. zeae strain WH1. However, the pure WH1 culture presented severe pathogenicity. Multilocus sequence analysis (MLSA) indicated that strains WH1, EC1, and EC2 isolated from rice were grouped into a clade differentiated from other D. zeae strains. The average nucleotide identity (ANI) and DNA-DNA hybridization (DDH) analyses demonstrated that WH1 was phylogenetically closest to EC2. Furthermore, the pathogenicity determinants and virulence factors of WH1 were mainly analyzed through genomic comparison with complete genomes of other D. zeae strains with high virulence (EC1, EC2, MS1, and MS2). The results revealed that plant cell wall-degrading extracellular enzymes (PCWDEs), flagellar and chemotaxis, and quorum sensing were highly conserved in all analyzed genomes, which were confirmed through phenotypic assays. Besides, WH1 harbored type I, II, III, and VI secretion systems (T1SS, T2SS, T3SS, and T6SS), but lost T4SS and T5SS. Like strains MS1 and MS2 isolated from bananas, WH1 harbored genes encoding both capsule polysaccharide (CPS) and exopolysaccharide (EPS) biosynthesis. The results of pathogenicity assays demonstrated that WH1 produced severe soft rot symptoms on potato tubers, carrots, radishes, and Chinese cabbage. Meanwhile, WH1 also produced phytotoxin(s) to inhibit rice seed germination with an 87% inhibitory rate in laboratory conditions. More importantly, we confirmed that phytotoxin(s) produced by WH1 are different from zeamines produced by EC1. Comparative genomics analyses and phenotypic and pathogenicity assays suggested that WH1 likely evolved through a pathway different from the other D. zeae strains from rice, producing a new type of rice foot rot pathogen. These findings highlight the emergence of a new type of D. zeae strain with high virulence, causing soft rot in rice and other plants.

The evolution of manipulative cheating

A social cheat is typically assumed to be an individual that does not perform a cooperative behaviour, or performs less of it, but can still exploit the cooperative behaviour of others. However, empirical data suggests that cheating can be more subtle, involving evolutionary arms races over the ability to both exploit and resist exploitation. These complications have not been captured by evolutionary theory, which lags behind empirical studies in this area. We bridge this gap with a mixture of game-theoretical models and individual-based simulations, examining what conditions favour more elaborate patterns of cheating. We found that as well as adjusting their own behaviour, individuals can be selected to manipulate the behaviour of others, which we term 'manipulative cheating'. Further, we found that manipulative cheating can lead to dynamic oscillations (arms races), between selfishness, manipulation, and suppression of manipulation. Our results can help explain both variation in the level of cheating, and genetic variation in the extent to which individuals can be exploited by cheats.

Scale-dependent environmental effects on phenotypic distributions in Heliconius butterflies

Identifying the relative importance of different mechanisms responsible for the emergence and maintenance of phenotypic diversity can be challenging, as multiple selective pressures and stochastic events are involved in these processes. Therefore, testing how environmental conditions shape the distribution of phenotypes can offer important insights on local adaptation, divergence, and speciation. The red-yellow Müllerian mimicry ring of Heliconius butterflies exhibits a wide diversity of color patterns across the Neotropics and is involved in multiple hybrid zones, making it a powerful system to investigate environmental drivers of phenotypic distributions. Using the distantly related Heliconius erato and Heliconius melpomene co-mimics and a multiscale distribution approach, we investigated whether distinct phenotypes of these species are associated with different environmental conditions. We show that Heliconius red-yellow phenotypic distribution is strongly driven by environmental gradients (especially thermal and precipitation variables), but that phenotype and environment associations vary with spatial scale. While co-mimics are usually predicted to occur in similar environments at large spatial scales, patterns at local scales are not always consistent (i.e., different variables are best predictors of phenotypic occurrence in different locations) or congruent (i.e., co-mimics show distinct associations with environment). We suggest that large-scale analyses are important for identifying how environmental factors shape broad mimetic phenotypic distributions, but that local studies are essential to understand the context-dependent biotic, abiotic, and historical mechanisms driving finer-scale phenotypic transitions.

A multiple phenotype imputation method for genetic diversity and core collection in Taiwanese vegetable soybean

Establishment of vegetable soybean (edamame) [Glycine max (L.) Merr.] germplasms has been highly valued in Asia and the United States owing to the increasing market demand for edamame. The idea of core collection (CC) is to shorten the breeding program so as to improve the availability of germplasm resources. However, multidimensional phenotypes typically are highly correlated and have different levels of missing rate, often failing to capture the underlying pattern of germplasms and select CC precisely. These are commonly observed on correlated samples. To overcome such scenario, we introduced the "multiple imputation" (MI) method to iteratively impute missing phenotypes for 46 morphological traits and jointly analyzed high-dimensional imputed missing phenotypes (EC impu ) to explore population structure and relatedness among 200 Taiwanese vegetable soybean accessions. An advanced maximization strategy with a heuristic algorithm and PowerCore was used to evaluate the morphological diversity among the EC impu . In total, 36 accessions (denoted as CC impu ) were efficiently selected representing high diversity and the entire coverage of the EC impu . Only 4 (8.7%) traits showed slightly significant differences between the CC impu and EC impu . Compared to the EC impu , 96% traits retained all characteristics or had a slight diversity loss in the CC impu . The CC impu exhibited a small percentage of significant mean difference (4.51%), and large coincidence rate (98.1%), variable rate (138.76%), and coverage (close to 100%), indicating the representativeness of the EC impu . We noted that the CC impu outperformed the CC raw in evaluation properties, suggesting that the multiple phenotype imputation method has the potential to deal with missing phenotypes in correlated samples efficiently and reliably without re-phenotyping accessions. Our results illustrated a significant role of imputed missing phenotypes in support of the MI-based framework for plant-breeding programs.

Phenotypic and genetic diversity of domestic yak (Bos grunniens) in high-altitude rangelands of Gilgit-Baltistan, Pakistan

Due to climate change, irrigated agriculture may become restricted in the mountain valleys in northern Pakistan in the future. Hence, the importance of yak (Bos grunniens) keeping in the mountain ranges as risk-mitigating strategy for mountain dwellers will potentially increase. However, little is known about the current status of the domestic yak in this region. We therefore used phenotypic characteristics and 13 microsatellite loci to determine the phenotypic differences and the level of genetic differentiation between populations of six valleys. Larger body measures and partially different physical appearance were observed in Shimshal and Khaplu yaks, especially when compared with yaks in the Chapurson valley. Overall, the mean observed heterozygosity was similar to the mean expected heterozygosity. Average genetic diversity was highest in the Hopar population and lowest in the Haramosh population. A low F_IS value indicated that individuals were less related than expected under a model of random mating. Three distinct genetic clusters were found for the six yak populations under study. Genetic distances were largest between Shimshal and Khaplu populations, and lowest between populations of Phandar and Hopar. It is concluded that yaks of Shimshal, Khaplu and Haramosh valleys were genetically distinct from yak populations in Chapurson, Hopar and Phandar valleys, indicating that the free-range conditions and pastoral yak rearing system in the region have preserved the underlying genetic diversity of the yak populations.

Diversity and Agronomic Performance of Lupinus mutabilis Germplasm in European and Andean Environments

The introduction of Lupinus mutabilis (Andean lupin) in Europe will provide a new source of protein and oil for plant-based diets and biomass for bio-based products, while contributing to the improvement of marginal soils. This study evaluates for the first time the phenotypic variability of a large panel of L. mutabilis accessions both in their native environment and over two cropping conditions in Europe (winter crop in the Mediterranean region and summer crop in North-Central Europe), paving the way for the selection of accessions adapted to specific environments. The panel of 225 accessions included both germplasm pools from the Andean region and breeding lines from Europe. Notably, we reported higher grain yield in Mediterranean winter-cropping conditions (18 g/plant) than in the native region (9 g/plant). Instead, North European summer-cropping conditions appear more suitable for biomass production (up to 2 kg/plant). The phenotypic evaluation of 16 agronomical traits revealed significant variation in the panel. Principal component analyses pointed out flowering time, yield, and architecture-related traits as the main factors explaining variation between accessions. The Peruvian material stands out among the top-yielding accessions in Europe, characterized by early lines with high grain yield (e.g., LIB065, LIB072, and LIB155). Bolivian and Ecuadorian materials appear more valuable for the selection of genotypes for Andean conditions and for biomass production in Europe. We also observed that flowering time in the different environments is influenced by temperature accumulation. Within the panel, it is possible to identify both early and late genotypes, characterized by different thermal thresholds (600°C-700°C and 1,000-1,200°C GDD, respectively). Indications on top-yielding and early/late accessions, heritability of morpho-physiological traits, and their associations with grain yield are reported and remain largely environmental specific, underlining the importance of selecting useful genetic resources for specific environments. Altogether, these results suggest that the studied panel holds the genetic potential for the adaptation of L. mutabilis to Europe and provide the basis for initiating a breeding program based on exploiting the variation described herein.

Climate shapes the spatiotemporal variation in color morph diversity and composition across the distribution range of Chrysomela lapponica leaf beetle

Color polymorphism offers rich opportunities for studying the eco-evolutionary mechanisms that drive the adaptations of local populations to heterogeneous and changing environments. We explored the color morph diversity and composition in a Chrysomela lapponica leaf beetle across its entire distribution range to test the hypothesis that environmental and climatic variables shape spatiotemporal variation in the phenotypic structure of a polymorphic species. We obtained information on 13 617 specimens of this beetle from museums, private collections, and websites. These specimens (collected from 1830-2020) originated from 959 localities spanning 33° latitude, 178° longitude, and 4200 m altitude. We classified the beetles into five color morphs and searched for environmental factors that could explain the variation in the level of polymorphism (quantified by the Shannon diversity index) and in the relative frequencies of individual color morphs. The highest level of polymorphism was found at high latitudes and altitudes. The color morphs differed in their climatic requirements; composition of colour morphs was independent of the geographic distance that separated populations but changed with collection year, longitude, mean July temperature and between-year temperature fluctuations. The proportion of melanic beetles, in line with the thermal melanism hypothesis, increased with increasing latitude and altitude and decreased with increasing climate seasonality. Melanic morph frequencies also declined during the past century, but only at high latitudes and altitudes where recent climate warming was especially strong. The observed patterns suggest that color polymorphism is especially advantageous for populations inhabiting unpredictable environments, presumably due to the different climatic requirements of coexisting color morphs.

Response of a Diverse European Soybean Collection to "Short Duration" and "Long Duration" Drought Stress

Drought causes significant damage to a high value crop of soybean. Europe has an increasing demand for soybean and its own production is insufficient. Selection and breeding of cultivars adapted to European growth conditions is therefore urgently needed. These new cultivars must have a shorter growing cycle (specifically for adaptation to North-West Europe), high yield potential under European growing conditions, and sufficient drought resistance. We have evaluated the performance of a diverse collection of 359 soybean accessions under drought stress using rain-out shelters for 2 years. The contrasting weather conditions between years and correspondingly the varying plant responses demonstrated that the consequences of drought for an individual accession can vary strongly depending on the characteristics (e.g., duration and intensity) of the drought period. Short duration drought stress, for a period of four to 7 weeks, caused an average reduction of 11% in maximum canopy height (CH), a reduction of 17% in seed number per plant (SN) and a reduction of 16% in seed weight per plant (SW). Long duration drought stress caused an average reduction of 29% in CH, a reduction of 38% in SN and a reduction of 43% in SW. Drought accelerated plant development and caused an earlier cessation of flowering and pod formation. This seemed to help some accessions to better protect the seed yield, under short duration drought stress. Drought resistance for yield-related traits was associated with the maintenance of growth under long duration drought stress. The collection displayed a broad range of variation for canopy wilting and leaf senescence but a very narrow range of variation for crop water stress index (CWSI; derived from canopy temperature data). To the best of our knowledge this is the first study reporting a detailed investigation of the response to drought within a diverse soybean collection relevant for breeding in Europe.

Genomic Comparisons and Phenotypic Diversity of Dickeya zeae Strains Causing Bacterial Soft Rot of Banana in China

Bacterial soft rot of banana, caused by Dickeya zeae, is spreading rapidly in important banana growing areas in China and seriously threatens banana production. In this study, we sequenced the high-quality complete genomes of three typical banana strains, MS1 (size: 4,831,702-bp; genome coverages: 538x), MS_2014 (size: 4,740,000-bp; genome coverages: 586x) and MS_2018 (size: 4,787,201-bp; genome coverages: 583x), isolated in 2009, 2014, and 2018, respectively. To determine their genomic and phenotypic diversity with respect to their hosts of origin, they were compared with other D. zeae strains, including another representative banana strain MS2 from China. The sequenced strains were similar in utilization of carbon source and chemical substrates, and general genomic features of GC content, and tRNA and rRNA regions. They were also conserved in most virulence determinants, including gene-encoding secretion systems, plant cell wall degrading enzymes, and exopolysaccharides. We further explored their genomic diversity in the predicted genomic islands (GIs). These GIs were rich in integrases and transposases, where some genomic dissimilarity was observed in the flagellar gene cluster and several secondary metabolite gene clusters. Different constituents of core biosynthetic modules were found within the bacteriocin and aryl polyene (APE) pigment gene clusters, and the strains from banana showed different phenotypes with respect to antibiosis effects and colony pigmentation. Additionally, clustered regularly interspaced short palindromic repeat (CRISPR) and prophage elements, such as type I-F and III-A CRISPR arrays and an intact prophage of MS1-P5, contributed to bacterial diversity. Phylogenetic tree analysis and genome-genome nucleotide comparison confirmed the genomic divergence among the strains isolated from banana. Considering these characteristics, MS2 and MS_2014 probably diverged later than MS1, while MS_2018 was different and more similar to foreign strains isolated from other hosts in several characteristics. Strain MS_2018 caused severe symptoms on banana varieties previously considered moderately resistant or moderately susceptible, including varieties of Cavendish (Musa AAA) and Plantain (Musa ABB). Our study of genomic and phenotypic diversity raises public attention to the risk of spreading new pathogenic variants within banana growing regions and supports development of predictive strategies for disease control.

Spatial modulation of individual behaviors enables an ordered structure of diverse phenotypes during bacterial group migration

Coordination of diverse individuals often requires sophisticated communications and high-order computational abilities. Microbial populations can exhibit diverse individualistic behaviors, and yet can engage in collective migratory patterns with a spatially sorted arrangement of phenotypes. However, it is unclear how such spatially sorted patterns emerge from diverse individuals without complex computational abilities. Here, by investigating the single-cell trajectories during group migration, we discovered that, despite the constant migrating speed of a group, the drift velocities of individual bacteria decrease from the back to the front. With a Langevin-type modeling framework, we showed that this decreasing profile of drift velocities implies the spatial modulation of individual run-and-tumble random motions, and enables the bacterial population to migrate as a pushed wave front. Theoretical analysis and stochastic simulations further predicted that the pushed wave front can help a diverse population to stay in a tight group, while diverse individuals perform the same type of mean reverting processes around centers orderly aligned by their chemotactic abilities. This mechanism about the emergence of orderly collective migration from diverse individuals is experimentally demonstrated by titration of bacterial chemoreceptor abundance. These results reveal a simple computational principle for emergent ordered behaviors from heterogeneous individuals.

Organisms living in large groups often have to move together in order to navigate, forage for food, and increase their roaming range. Such groups are often made up of distinct individuals that must integrate their different behaviors in order to migrate in the same direction at a similar pace. For instance, for the bacteria Escherichia coli to travel as a condensed group, they must coordinate their response to a set of chemical signals called chemoattractants that tell them where to go.

The chemoattractants surrounding the bacteria are unequally distributed so that there is more of them at the front than the back of the group. During migration, each bacterium moves towards this concentration gradient in a distinct way, spontaneously rotating its direction in a ‘run-and-tumble’ motion that guides it towards areas where there are high levels of these chemical signals. In addition to this variability, how well individual bacteria are able to swim up the gradient also differs within the population. Bacteria that are better at sensing the chemoattractant gradient are placed at the front of the group, while those that are worst are shifted towards the back. This spatial arrangement is thought to help the bacteria migrate together. But how E. coli organize themselves in to this pattern is unclear, especially as they cannot communicate directly with one another and display such diverse, randomized behaviors.

To help answer this question, Bai, He et al. discovered a general principle that describes how single bacterial cells move within a group. The results showed that E. coli alter their run-and-tumble motion depending on where they reside within the population: individuals at the rear drift faster so they can catch up with the group, while those leading the group drift slower to draw themselves back. This ‘reversion behavior’ allows the migrating bacteria to travel at a constant speed around a mean position relative to the group.

A cell’s drifting speed is determined by how well it moves towards the chemoattractant and its response to the concentration gradient. As a result, the mean position around which the bacterium accelerates or deaccelerates will vary depending on how sensitive it is to the chemoattractant gradient. The E. coli therefore spatially arrange themselves so that the more sensitive bacteria are located at the front of the group where the gradient is shallower; and cells that are less sensitive are located towards the back where the gradient is steeper.

These findings suggest a general principle for how bacteria form ordered patterns whilst migrating as a collective group. This behavior could also apply to other populations of distinct individuals, such as ants following a trail or flocks of birds migrating in between seasons.

Pitfalls in the Diagnosis of β-Thalassemia Intermedia

We present case histories of three patients who had β-thalassemia (β-thal) trait with 'unusual severity' managed as β-thal intermedia (β-TI) where the basis of disease severity could not be explained with routine hematological and genetic investigations. The clinical diagnosis of 'thalassemia intermedia' was justifiable as they had a β-thal mutation and disease severity that did not fit in with either β-thal trait or with β-thal major (β-TM). As mutations of α, β, and γ genes could not explain the unusual severity of the disease, further analysis with next-generation sequencing (NGS) for red cell diseases was carried out, which led to the diagnosis of coexisting membranopathies. This case series highlights the inherent difficulty in the diagnosis of β-TI with certainty in some patients where the genetic basis is not clear-cut.

Flow cytometric monitoring of the bacterial phenotypic diversity in aquatic ecosystems

Flow cytometry is a promising tool used to identify the phenotypic features of bacterial communities in aquatic ecosystems by measuring the physical and chemical properties of cells based on their light scattering behavior and fluorescence. Compared to molecular or culture-based approaches, flow cytometry is suitable for the online monitoring of microbial water quality because of its relatively simple sample preparation process, rapid analysis time, and high-resolution phenotypic data. Advanced statistical techniques (e.g., denoising and binning) can be utilized to successfully calculate phenotypic diversity by processing the scatter data obtained from flow cytometry. These phenotypic diversities were well correlated with taxonomic-based diversity computed using next-generation 16S RNA gene sequencing. The protocol provided in this paper should be a useful guide for a fast and reliable flow cytometric monitoring of bacterial phenotypic diversity in aquatic ecosystems.

Local adaptation optimizes photoprotection strategies in a Neotropical legume tree under drought stress

Photoprotection is a plant functional mechanism to prevent photooxidative damage by excess light. This is most important when carbon assimilation is limited by drought, and as such, it entails a trade-off between carbon assimilation vs stress avoidance. The ecological adaptation of plants to local water availability can lead to different photoprotective strategies. To test this, we used different provenances of Caesalpinia spinosa (Mol.) Kuntze (commonly known as 'tara') along a precipitation gradient. Tara is a Neotropical legume tree with high ecological and commercial value, found in dry tropical forests, which are increasingly threatened by climate change. Morphological and physiological responses of tara provenances were analysed under three different treatments of drought and leaflet immobilization, i.e., light stress, in a common garden greenhouse experiment. Tara quickly responded to drought by reducing stomatal conductance, evapotranspiration, photochemical efficiency, carbon assimilation and growth, while increasing structural and chemical photoprotection (leaflet angle and pigments for thermal dissipation). Leaflet closure was an efficient photoprotection strategy with overall physiological benefits for seedlings as it diminished the evaporative demand and avoided photodamage, but also entailed costs by reducing net carbon assimilation opportunities. These responses depended on seed origin, with seedlings from the most xeric locations showing the highest dehydration tolerance, suggesting local adaptation and highlighting the value of different strategies under distinct environments. This plasticity in its response to environmental stress allows tara to thrive in locations with contrasting water availability. Our findings increase the understanding of the factors controlling the functional ecology of tara in response to drought, which can be leveraged to improve forecasts of changes in its distribution range, and for planning restoration projects with this keystone tree species.

Identification of new ethanol-tolerant yeast strains with fermentation potential from central Patagonia

The quest for new wild yeasts has increasingly gained attention because of their potential ability to provide unique organoleptic characters to fermented beverages. In this sense, Patagonia offers a wide diversity of ethanol-tolerant yeasts and stands out as a bioprospecting alternative. This study characterized the genetic and phenotypic diversity of yeast isolates obtained from Central Chilean Patagonia and analyzed their fermentation potential under different fermentative conditions. We recovered 125 colonies from Nothofagus spp. bark samples belonging to five yeast species: Saccharomyces eubayanus, Saccharomyces uvarum, Lachancea cidri, Kregervanrija delftensis, and Hanseniaspora valbyensis. High-throughput microcultivation assays demonstrated the extensive phenotypic diversity among Patagonian isolates, where Saccharomyces spp and L. cidri isolates exhibited the most outstanding fitness scores across the conditions tested. Fermentation performance assays under wine, mead, and beer conditions demonstrated the specific potential of the different species for each particular beverage. Saccharomyces spp. were the only isolates able to ferment beer wort. Interestingly, we found that L. cidri is a novel candidate species to ferment wine and mead, exceeding the fermentation capacity of a commercial strain. Unlike commercial strains, we found that L. cidri does not require nutritional supplements for efficient mead fermentation. In addition, L. cidri produces succinic and acetic acids, providing a distinct profile to the final fermented product. This work demonstrates the importance of bioprospecting efforts in Patagonia to isolate novel wild yeast strains with extraordinary biotechnological potential for the fermentation industry.

Genetic and Phenotypic Diversities in Experimental Populations of Diploid Inter-Lineage Hybrids in the Human Pathogenic Cryptococcus

To better understand the potential factors contributing to genome instability and phenotypic diversity, we conducted mutation accumulation (MA) experiments for 120 days for 7 diploid cryptococcal hybrids under fluconazole (10 MA lines each) and non-fluconazole conditions (10 MA lines each). The genomic DNA content, loss of heterozygosity (LOH) rate, growth ability, and fluconazole susceptibility were determined for all 140 evolved cultures. Compared to that of their ancestral clones, the evolved clones showed: (i) genomic DNA content changes ranging from ~22% less to ~27% more, and (ii) reduced, similar, and increased phenotypic values for each tested trait, with most evolved clones displaying increased growth at 40 °C and increased fluconazole resistance. Aside from the ancestral multi-locus genotypes (MLGs) and heterozygosity patterns (MHPs), 77 unique MLGs and 70 unique MPHs were identified among the 140 evolved cultures at day 120. The average LOH rates of the MA lines in the absence and presence of fluconazole were similar at 1.27 × 10⁻⁴ and 1.38 × 10⁻⁴ LOH events per MA line per mitotic division, respectively. While LOH rates varied among MA lines from different ancestors, there was no apparent correlation between the genetic divergence of the parental haploid genomes within ancestral clones and LOH rates. Together, our results suggest that hybrids between diverse lineages of the human pathogenic Cryptococcus can generate significant genotypic and phenotypic diversities during asexual reproduction.

Non-Genetic Diversity in Chemosensing and Chemotactic Behavior

Non-genetic phenotypic diversity plays a significant role in the chemotactic behavior of bacteria, influencing how populations sense and respond to chemical stimuli. First, we review the molecular mechanisms that generate phenotypic diversity in bacterial chemotaxis. Next, we discuss the functional consequences of phenotypic diversity for the chemosensing and chemotactic performance of single cells and populations. Finally, we discuss mechanisms that modulate the amount of phenotypic diversity in chemosensory parameters in response to changes in the environment.

Plastic rewiring of Sef1 transcriptional networks and the potential of non-functional transcription factor binding in facilitating adaptive evolution

Prior and extensive plastic rewiring of a transcriptional network, followed by a functional switch of the conserved transcriptional regulator, can shape the evolution of a new network with diverged functions. The presence of three distinct iron regulatory systems in fungi that use orthologous transcriptional regulators suggests that these systems evolved in that manner. Orthologs of the transcriptional activator Sef1 are believed to be central to how iron regulatory systems developed in fungi, involving gene gain, plastic network rewiring, and switches in regulatory function. We show that, in the protoploid yeast Lachancea kluyveri, plastic rewiring of the L. kluyveri Sef1 (Lk-Sef1) network, together with a functional switch, enabled Lk-Sef1 to regulate TCA cycle genes, unlike Candida albicans Sef1 that mainly regulates iron-uptake genes. Moreover, we observed pervasive nonfunctional binding of Sef1 to its target genes. Enhancing Lk-Sef1 activity resuscitated the corresponding transcriptional network, providing immediate adaptive benefits in changing environments. Our study not only sheds light on the evolution of Sef1-centered transcriptional networks but also shows the adaptive potential of nonfunctional transcription factor binding for evolving phenotypic novelty and diversity.

Demographic and ecogeographic factors limit wild grapevine spread at the southern edge of its distribution range

The spatial distribution of plants is constrained by demographic and ecogeographic factors that determine the range and abundance of the species. Wild grapevine (Vitis vinifera ssp. sylvestris) is distributed from Switzerland in the north to Israel in the south. However, little is known about the ecogeographic constraints of this species and its genetic and phenotypic characteristics, especially at the southern edge of its distribution range in the Levant region. In this study, we explore the population structure of southern Levantine wild grapevines and the correlation between demographic and ecogeographic characteristics. Based on our genetic analysis, the wild grapevine populations in this region can be divided into two major subgroups in accordance with a multivariate spatial and ecogeographical clustering model. The identified subpopulations also differ in morphological traits, mainly leaf hairiness which may imply adaptation to environmental stress. The findings suggest that the Upper Jordan River population was spread to the Sea of Galilee area and that a third smaller subpopulation at the south of the Golan Heights may represent a distinguished gene pool or a recent establishment of a new population. A spatial distribution model indicated that distance to water sources, Normalized difference vegetation index, and precipitation are the main environmental factors constraining V. v. sylvestris distribution at its southern distribution range. These factors in addition to limited gene flow between populations prevent further spread of wild grapevines southwards to semi-arid regions.

Single-cell image analysis to explore cell-to-cell heterogeneity in isogenic populations

Single-cell image analysis provides a powerful approach for studying cell-to-cell heterogeneity, which is an important attribute of isogenic cell populations, from microbial cultures to individual cells in multicellular organisms. This phenotypic variability must be explained at a mechanistic level if biologists are to fully understand cellular function and address the genotype-to-phenotype relationship. Variability in single-cell phenotypes is obscured by bulk readouts or averaging of phenotypes from individual cells in a sample; thus, single-cell image analysis enables a higher resolution view of cellular function. Here, we consider examples of both small- and large-scale studies carried out with isogenic cell populations assessed by fluorescence microscopy, and we illustrate the advantages, challenges, and the promise of quantitative single-cell image analysis.

Comparative genomics reveals an SNP potentially leading to phenotypic diversity of Salmonella enterica serovar Enteritidis

An SNP is a spontaneous genetic change having a potential to modify the functions of the original genes and to lead to phenotypic diversity of bacteria in nature. In this study, a phylogenetic analysis of Salmonella enterica serovar Enteritidis, a major food-borne pathogen, showed that eight strains of S. Enteritidis isolated in South Korea, including FORC_075 and FORC_078, have almost identical genome sequences. Interestingly, however, the abilities of FORC_075 to form biofilms and red, dry and rough (RDAR) colonies were significantly impaired, resulting in phenotypic differences among the eight strains. Comparative genomic analyses revealed that one of the non-synonymous SNPs unique to FORC_075 has occurred in envZ, which encodes a sensor kinase of the EnvZ/OmpR two-component system. The SNP in envZ leads to an amino acid change from Pro248 (CCG) in other strains including FORC_078 to Leu248 (CTG) in FORC_075. Allelic exchange of envZ between FORC_075 and FORC_078 identified that the SNP in envZ is responsible for the impaired biofilm- and RDAR colony-forming abilities of S. Enteritidis. Biochemical analyses demonstrated that the SNP in envZ significantly increases the phosphorylated status of OmpR in S. Enteritidis and alters the expression of the OmpR regulon. Phenotypic analyses further identified that the SNP in envZ decreases motility of S. Enteritidis but increases its adhesion and invasion to both human epithelial cells and murine macrophage cells. In addition to an enhancement of infectivity to the host cells, survival under acid stress was also elevated by the SNP in envZ. Together, these results suggest that the natural occurrence of the SNP in envZ could contribute to phenotypic diversity of S. Enteritidis, possibly improving its fitness and pathogenesis.

Phenotypic Diversity of 15q11.2 BP1-BP2 Deletion in Three Korean Families with Development Delay and/or Intellectual Disability: A Case Series and Literature Review

The 15q11.2 breakpoint (BP) 1–BP2 deletion syndrome is emerging as the most frequent pathogenic copy number variation in humans related to neurodevelopmental diseases, with changes in cognition, behavior, and brain morphology. Previous publications have reported that patients with 15q11.2 BP1–BP2 deletion showed intellectual disability (ID), speech impairment, developmental delay (DD), and/or behavioral problems. We describe three new cases, aged 3 or 6 years old and belonging to three unrelated Korean families, with a 350-kb 15q11.2 BP1–BP2 deletion of four highly conserved genes, namely, the TUBGCP5, CYFIP1, NIPA2, and NIPA1 genes. All of our cases presented with global DD and/or ID, and the severity ranged from mild to severe, but common facial dysmorphism and congenital malformations in previous reports were not characteristic. The 15q11.2 BP1–BP2 deletion was inherited from an unaffected parent in all cases. Our three cases, together with previous findings from the literature review, confirm some of the features earlier reported to be associated with 15q11.2 BP1–BP2 deletion and help to further delineate the phenotype associated with 15q11.2 deletion. Identification of more cases with 15q11.2 BP1–BP2 deletion will allow us to obtain a better understanding of the clinical phenotypes. Further explanation of the functions of the genes within the 15q11.2 BP1–BP2 region is required to resolve the pathogenic effects on neurodevelopment.

Characterization of the Genetic Diversity Present in a Diverse Sesame Landrace Collection Based on Phenotypic Traits and EST-SSR Markers Coupled With an HRM Analysis

A selection of sesame (Sesamum indicum L.) landraces of different eco-geographical origin and breeding history have been characterized using 28 qualitative morpho-physiological descriptors and seven expressed sequence tag-simple sequence repeat (EST-SSR) markers coupled with a high-resolution melting (HRM) analysis. The most variable qualitative traits that could efficiently discriminate landraces, as revealed by the correlation analyses, were the plant growth type and position of the branches, leaf blade width, stem pubescence, flowering initiation, capsule traits and seed coat texture. The agglomerative hierarchical clustering analysis based on a dissimilarity matrix highlighted three main groups among the sesame landraces. An EST-SSR marker analysis revealed an average polymorphism information content (PIC) value of 0.82, which indicated that the selected markers were highly polymorphic. A principal coordinate analysis and dendrogram reconstruction based on the molecular data classified the sesame genotypes into four major clades. Both the morpho-physiological and molecular analyses showed that landraces from the same geographical origin were not always grouped in the same cluster, forming heterotic groups; however, clustering patterns were observed for the Greek landraces. The selective breeding of such traits could be employed to unlock the bottleneck of local phenotypic diversity and create new cultivars with desirable traits.

Phenotypic Diversity of Cardiomyopathy Caused by an MYBPC3 Frameshift Mutation in a Korean Family: A Case Report

Restrictive cardiomyopathy (RCM) is one of the rarest cardiac disorders, with a very poor prognosis, and heart transplantation is the only long-term treatment of choice. We reported that a Korean family presented different cardiomyopathies, such as idiopathic RCM and hypertrophic cardiomyopathy (HCM), caused by the same MYBPC3 mutation in different individuals. A 74-year-old male was admitted for the evaluation of exertional dyspnea, palpitations, and pitting edema in both legs for several months. Transthoracic echocardiography (TTE) showed RCM with biatrial enlargement and pericardial effusion. Cardiac magnetic resonance (CMR) images revealed normal left ventricular chamber size, borderline diffuse left ventricular hypertrophy and very large atria. In contrast to the proband, CMR images showed asymmetric septal hypertrophy of the left ventricle, consistent with a diagnosis of HCM in the proband’s two daughters. Of the five heterozygous variants identified as candidate causes of inherited cardiomyopathy by whole exome sequencing in the proband, Sanger sequencing confirmed the presence of a heterozygous frameshift mutation (NM_000256.3:c.3313_3314insGG; p.Ala1105Glyfs*85) in MYBPC3 in the proband and his affected daughters, but not in his unaffected granddaughter. There is clinical and genetic overlap of HCM with restrictive physiology and RCM, especially when HCM is combined with severe myocardial fibrosis. Family screening with genetic testing and CMR imaging could be excellent tools for the evaluation of idiopathic RCM.

Variation in the life history strategy underlies functional diversity of tumors

Classical r- vs. K-selection theory describes the trade-offs between high reproductive output and competitiveness and guides research in evolutionary ecology. While its impact has waned in the recent past, cancer evolution may rekindle it. Herein, we impose r- or K-selection on cancer cell lines to obtain strongly proliferative r cells and highly competitive K cells to test ideas on life-history strategy evolution. RNA-seq indicates that the trade-offs are associated with distinct expression of genes involved in the cell cycle, adhesion, apoptosis, and contact inhibition. Both empirical observations and simulations based on an ecological competition model show that the trade-off between cell proliferation and competitiveness can evolve adaptively. When the r and K cells are mixed, they exhibit strikingly different spatial and temporal distributions. Due to this niche separation, the fitness of the entire tumor increases. The contrasting selective pressure may operate in a realistic ecological setting of actual tumors.

Prenatal detection of distal 1q21.1q21.2 microduplication with abnormal ultrasound findings: Two cases report and literature review

RATIONALE

1q21.1 duplication is an uncommon chromosomal submicroscopic imbalance which is associated with growth/mental retardation, dysmorphic features, autism, multiple congenital and neuropsychiatric disorders.

PATIENT CONCERNS

Two pregnant women underwent amniocentesis for cytogenetic analysis and chromosomal microarray analysis (CMA) following abnormal ultrasound findings. Case 1 presented short nasal bone and case 2 showed absent nasal bone, ventricular septal defect and umbilical cord circling in ultrasonic examination.

DIAGNOSES

G-banding analysis showed that the two fetuses presented normal karyotypic results while CMA detected 1.796 Mb (case 1) and 1.242 Mb (case 2) microduplications in the region of 1q21.1q21.2 separately. Furthermore, the CMA also revealed a 1.2 Mb microdeletion of 8p23.3 in case 1.

INTERVENTIONS

The couple in case 1 chose to terminate the pregnancy, while the couple in case 2 continued the pregnancy and finally delivered a male infant who presented low nasal bridge and ventricular septal defect.

OUTCOMES

The 1q21.1q21.2 duplications in our report were located in the distal 1q21.1 region, overlapping with 1q21.1 duplication syndrome. Case 2 was the first reported live birth with 1q21.1 duplication according to prenatal CMA detection in China.

LESSONS

The genotype-phenotype of 1q21.1 duplication is complicated due to the phenotypic diversity, incomplete penetrance, and lack of obvious characteristics. So it is difficult to predict the postnatal development and health conditions clinically. Hence, long term follow up is necessary for newborn infants with 1q21.1 duplication, irrespective of whether the duplication is de novo or inherited.

Raman Spectroscopy-Based Measurements of Single-Cell Phenotypic Diversity in Microbial Populations

Microbial cells that live in the same community can exist in different physiological and morphological states that change as a function of spatiotemporal variations in environmental conditions. This phenomenon is commonly known as phenotypic heterogeneity and/or diversity. Measuring this plethora of cellular expressions is needed to better understand and manage microbial processes. However, most tools to study phenotypic diversity only average the behavior of the sampled community. In this work, we present a way to quantify the phenotypic diversity of microbial samples by inferring the (bio)molecular profile of its constituent cells using Raman spectroscopy. We demonstrate how this tool can be used to quantify the phenotypic diversity that arises after the exposure of microbes to stress. Raman spectroscopy holds potential for the detection of stressed cells in bioproduction.

Microbial cells experience physiological changes due to environmental change, such as pH and temperature, the release of bactericidal agents, or nutrient limitation. This has been shown to affect community assembly and physiological processes (e.g., stress tolerance, virulence, or cellular metabolic activity). Metabolic stress is typically quantified by measuring community phenotypic properties such as biomass growth, reactive oxygen species, or cell permeability. However, bulk community measurements do not take into account single-cell phenotypic diversity, which is important for a better understanding and the subsequent management of microbial populations. Raman spectroscopy is a nondestructive alternative that provides detailed information on the biochemical makeup of each individual cell. Here, we introduce a method for describing single-cell phenotypic diversity using the Hill diversity framework of Raman spectra. Using the biomolecular profile of individual cells, we obtained a metric to compare cellular states and used it to study stress-induced changes. First, in two Escherichia coli populations either treated with ethanol or nontreated and then in two Saccharomyces cerevisiae subpopulations with either high or low expression of a stress reporter. In both cases, we were able to quantify single-cell phenotypic diversity and to discriminate metabolically stressed cells using a clustering algorithm. We also described how the lipid, protein, and nucleic acid compositions changed after the exposure to the stressor using information from the Raman spectra. Our results show that Raman spectroscopy delivers the necessary resolution to quantify phenotypic diversity within individual cells and that this information can be used to study stress-driven metabolic diversity in microbial populations.

IMPORTANCE Microbial cells that live in the same community can exist in different physiological and morphological states that change as a function of spatiotemporal variations in environmental conditions. This phenomenon is commonly known as phenotypic heterogeneity and/or diversity. Measuring this plethora of cellular expressions is needed to better understand and manage microbial processes. However, most tools to study phenotypic diversity only average the behavior of the sampled community. In this work, we present a way to quantify the phenotypic diversity of microbial samples by inferring the (bio)molecular profile of its constituent cells using Raman spectroscopy. We demonstrate how this tool can be used to quantify the phenotypic diversity that arises after the exposure of microbes to stress. Raman spectroscopy holds potential for the detection of stressed cells in bioproduction.

Functional diversity of small-mammal postcrania is linked to both substrate preference and body size

Selective pressures favor morphologies that are adapted to distinct ecologies, resulting in trait partitioning among ecomorphotypes. However, the effects of these selective pressures vary across taxa, especially because morphology is also influenced by factors such as phylogeny, body size, and functional trade-offs. In this study, we examine how these factors impact functional diversification in mammals. It has been proposed that trait partitioning among mammalian ecomorphotypes is less pronounced at small body sizes due to biomechanical, energetic, and environmental factors that favor a “generalist” body plan, whereas larger taxa exhibit more substantial functional adaptations. We title this the Divergence Hypothesis (DH) because it predicts greater morphological divergence among ecomorphotypes at larger body sizes. We test DH by using phylogenetic comparative methods to examine the postcranial skeletons of 129 species of taxonomically diverse, small-to-medium-sized (<15 kg) mammals, which we categorize as either “tree-dwellers” or “ground-dwellers.” In some analyses, the morphologies of ground-dwellers and tree-dwellers suggest greater between-group differentiation at larger sizes, providing some evidence for DH. However, this trend is neither particularly strong nor supported by all analyses. Instead, a more pronounced pattern emerges that is distinct from the predictions of DH: within-group phenotypic disparity increases with body size in both ground-dwellers and tree-dwellers, driven by morphological outliers among “medium”-sized mammals. Thus, evolutionary increases in body size are more closely linked to increases in within-locomotor-group disparity than to increases in between-group disparity. We discuss biomechanical and ecological factors that may drive these evolutionary patterns, and we emphasize the significant evolutionary influences of ecology and body size on phenotypic diversity.

The Israeli-Palestinian wheat landraces collection: restoration and characterization of lost genetic diversity

BACKGROUND

For over a century, genetic diversity of wheat worldwide was eroded by continual selection for high yields and industrial demands. Wheat landraces cultivated in Israel and Palestine demonstrate high genetic diversity and a potentially wide repertoire of adaptive alleles. While most Israeli-Palestinian wheat landraces were lost in the transition to 'Green Revolution' semi-dwarf varieties, some germplasm collections made at the beginning of the 20th century survived in gene banks and private collections worldwide. However, fragmentation and poor conservation place this unique genetic resource at a high risk of genetic erosion. Herein, we describe a long-term initiative to restore, conserve, and characterize a collection of Israeli and Palestinian wheat landraces (IPLR).

RESULTS

We report on (i) the IPLR construction (n = 932), (ii) the historical and agronomic context to this collection, (iii) the characterization and assessment of the IPLR's genetic diversity, and (iv) a data comparison from two distinct subcollections within IPLR: a collection made by N. Vavilov in 1926 (IPLR-VIR) and a later one (1979-1981) made by Y. Mattatia (IPLR-M). Though conducted in the same eco-geographic space, these two collections were subjected to considerably different conservation pathways. IPLR-M, which underwent only one propagation cycle, demonstrated marked genetic and phenotypic variability (within and between accessions) in comparison with IPLR-VIR, which had been regularly regenerated over ∼90 years.

CONCLUSION

We postulate that long-term ex situ conservation involving human and genotype × environment selection may significantly reduce accession heterogeneity and allelic diversity. Results are further discussed in a broader context of pre-breeding and conservation. © 2019 Society of Chemical Industry.

Variants at codon 838 in the GUCY2D gene result in different phenotypes of cone rod dystrophy

BACKGROUND

The GUCY2D gene encodes the photoreceptor guanylate cyclase (GC-E) and different pathogenic variants can lead to Leber congenital amaurosis (LCA) or cone-rod dystrophy (CRD). In this study, we describe three unrelated families who carried different mutations at codon 838 of the GUCY2D gene, and presented different phenotypes of retinal degeneration.

MATERIALS AND METHODS

Family and personal histories were collected, and the patients underwent best corrected visual acuity (BCVA), fundus photography (FP), electroretinography (ERG), optical coherence tomography (OCT) and fundus autofluorescence (FAF). Venous blood was drawn from patients and family members, and genomic DNA was extracted. Next-generation sequencing of known ocular genes was applied to the proband to find pathogenic variants. Polymerase chain reaction (PCR) and Sanger sequencing were conducted for validation and segregation.

RESULTS

Six patients from three unrelated families were enrolled. All the patients manifested decreased vision, photophobia and myopia from childhood. ERG recordings demonstrated a significant reduction in cone responses for all patients, while rod responses ranged widely from normal to moderately reduced. All patients were diagnosed with CRD, but the disease severity and progression rates in the three families were significantly different. Three pathogenic variants in the GUCY2D gene (c.2512 C > T (p.R838C), c.2512 C > A (p.R838S) and c.2513 G > A (p.R838H)) were identified.

CONCLUSIONS

We presented the phenotypes of three Chinese adCRD families carrying different variants at codon 838 of the GUCY2D gene. The R838S variant is a novel genotype associated with GUCY2D-CRD. The R838H variant can cause severe retinal features. Our findings enhance the understanding of GUCY2D phenotypic diversity.

Metabolic Heterogeneity and Cross-Feeding in Bacterial Multicellular Systems

Cells in assemblages differentiate and perform distinct roles. Though many pathways of differentiation are understood at the molecular level in multicellular eukaryotes, the elucidation of similar processes in bacterial assemblages is recent and ongoing. Here, we discuss examples of bacterial differentiation, focusing on cases in which distinct metabolisms coexist and those that exhibit cross-feeding, with one subpopulation producing substrates that are metabolized by a second subpopulation. We describe several studies of single-species systems, then segue to studies of multispecies metabolic heterogeneity and cross-feeding in the clinical setting. Many of the studies described exemplify the application of new techniques and modeling approaches that provide insights into metabolic interactions relevant for bacterial growth outside the laboratory.

Activation of Meiotic Genes Mediates Ploidy Reduction during Cryptococcal Infection

Cryptococcus neoformans is a global human fungal pathogen that causes fatal meningoencephalitis in mostly immunocompromised individuals. During pulmonary infection, cryptococcal cells form large polyploid cells that exhibit increased resistance to host immune attack and are proposed to contribute to the latency of cryptococcal infection. These polyploid titan cells can generate haploid and aneuploid progeny that may result in systemic infection. What triggers cryptococcal polyploidization and how ploidy reduction is achieved remain open questions. Here, we discovered that Cryptococcus cells polyploidize in response to genotoxic stresses that cause DNA double-strand breaks. Intriguingly, meiosis-specific genes are activated in C. neoformans and contribute to ploidy reduction, both in vitro and during infection in mice. Cryptococcal cells that activated their meiotic genes in mice were resistant to specific genotoxic stress compared to sister cells recovered from the same host tissue but without activation of meiotic genes. Our findings support the idea that meiotic genes, in addition to their conventional roles in classic sexual reproduction, contribute to adaptation of eukaryotic cells that undergo dramatic genome changes in response to genotoxic stress. The discovery has additional implications for evolution of sexual reproduction and the paradox of the presence of meiotic machinery in asexual species. Finally, our findings in this eukaryotic microbe mirror the revolutionary discoveries of the polyploidization and meiosis-like ploidy reduction process in cancer cells, suggesting that the reversible ploidy change itself could provide a general mechanism for rejuvenation to promote individual survival in response to stress.