Genome-wide deficiency mapping of the regions responsible for temporal canalization of the developmental processes of Drosophila melanogaster

Developmental processes of organisms are programed to proceed in a finely regulated manner and finish within a certain period of time depending on the ambient environmental conditions. Therefore, variation in the developmental period under controlled genetic and environmental conditions indicates innate instability of the developmental process. In this study, we aimed to determine whether a molecular machinery exists that regulates the canalization of the developmental period and, if so, to test whether the same mechanism also stabilizes a morphological trait. To search for regions that influence the instability of the developmental period, we conducted genome-wide deficiency mapping with 441 isogenic deficiency strains covering 65.5% of the Drosophila melanogaster genome. We found that 11 independent deficiencies significantly increased the instability of the developmental period and 5 of these also significantly increased the fluctuating asymmetry of wing shape although there was no significant correlation between the instabilities of developmental period and wing shape in general. These results suggest that canalization processes of the developmental period and morphological traits are at least partially independent. Our findings emphasize the potential importance of temporal variation in development as an indicator of developmental stability and canalization and provide a novel perspective for understanding the regulation of phenotypic variability

Natural genetic variation in fluctuating asymmetry of wing shape in Drosophila melanogaster

Fluctuating asymmetry (FA), defined as random deviation from perfect symmetry, has been used to assay the inability of individuals to buffer their developmental processes from environmental perturbations (i.e., developmental instability). In this study, we aimed to characterize the natural genetic variation in FA of wing shape in Drosophila melanogaster, collected from across the Japanese archipelago. We quantified wing shapes at whole wing and partial wing component levels and evaluated their mean and FA. We also estimated the heritability of the mean and FA of these traits. We found significant natural genetic variation in all the mean wing traits and in FA of one of the partial wing components. Heritability estimates for mean wing shapes were significant in two and four out of five wing traits in males and females, respectively. On the contrary, heritability estimates for FA were low and not significant. This is a novel study of natural genetic variation in FA of wing shape. Our findings suggest that partial wing components behave as distinct units of selection for FA, and local adaptation of the mechanisms to stabilize developmental processes occur in nature

Environmental Stress-Dependent Effects of Deletions Encompassing Hsp70Ba on Canalization and Quantitative Trait Asymmetry in Drosophila melanogaster

Hsp70 genes may influence the expression of wing abnormalities in Drosophila melanogaster but their effects on variability in quantitative characters and developmental instability are unclear. In this study, we focused on one of the six Hsp70 genes, Hsp70Ba, and investigated its effects on within-and among-individual variability in orbital bristle number, sternopleural bristle number, wing size and wing shape under different environmental conditions. To do this, we studied a newly constructed deletion, Df(3R)ED5579, which encompasses Hsp70Ba and nine non-Hsp genes, in the heterozygous condition and another, Hsp70Ba304, which deletes only Hsp70Ba, in the homozygous condition. We found no significant effect of both deletions on within-individual variation quantified by fluctuating asymmetry (FA) of morphological traits. On the other hand, the Hsp70Ba304/Hsp70Ba304 genotype significantly increased among-individual variation quantified by coefficient of variation (CV) of bristle number and wing size in female, while the Df(3R)ED5579 heterozygote showed no significant effect. The expression level of Hsp70Ba in the deletion heterozygote was 6 to 20 times higher than in control homozygotes, suggesting that the overexpression of Hsp70Ba did not influence developmental stability or canalization significantly. These findings suggest that the absence of expression of Hsp70Ba increases CV of some morphological traits and that HSP70Ba may buffer against environmental perturbations on some quantitative traits

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Abstract:  The study of the SARS-CoV-2 genome allows to evaluate its evolutionary pattern, identify mutations, lineages and variants that may have an impact on public health. Variants of concern (VOC) and variants of interest (VOI), which have different biological characteristics, have been identified worldwide. The objective of this work is to describe the lineages and variants of SARS-CoV-2 circulating in Córdoba using different strategies. Three strategies were implemented from positive SARS-CoV-2 RNA samples (Cts<30): 1)-whole genome sequencing (WGS) (ONT-MinION): 203 samples analysed from March 2020 to June 2021; 2)-partial sequencing of the Spike protein gene (Sanger): 54 samples analysed between February and April 2021 of travellers from abroad; and 3)-real time RT-PCR for detection of relevant VOC mutations (TaqMan™ SARS-CoV-2 Mutation Panel, Applied Biosystems): 816 samples analysed between May and June 2021.   Results were the following: 1)-circulation of 7 lineages with a greater predominance of B.1.1.33.3 (N3) (40.5%) and B.1.499 (38.8%), between March 2020 and January 2021; and circulation of 12 lineages with presence of VOC [P.1 (Gamma, 28.4%), B.1.1.7 (Alpha, 6.9%)] and VOI [C.37 (Lambda, 20.6%), B.1.427 (Epsilon, 10.8%), P2 (Zeta, 2.9%), B.1.526 (Iota, 2%)], between February and June 2021; 2)-presence of VOC Alpha (26.4%) and Gamma (17%), and samples compatible with VOI Epsilon and Zeta; 3)-presence of VOC Gamma (56%) and Alpha (11%), and other variants which could not be typified by this methodology. Results show the circulation of many SARS-CoV-2 lineages in Córdoba, which varied their distribution over time, according to the different introductions occurred, the population movement and the evolutionary advantages of some variants over others. In March 2021, the first VOC detections were realized in the province (Alpha and Gamma), being Gamma the one that mostly circulates at present. Although the WGS is the technique which provides more information, the other 2 strategies implemented were and are very useful tools for molecular epidemiological surveillance, obtaining the information in real time. Strategy 3 is a simpler, faster and more operative tool for molecular VOC screening.Resumen:  El estudio del genoma de SARS-CoV-2 permite evaluar su dinámica evolutiva, identificar mutaciones, linajes y variantes que puedan impactar en la salud pública. A nivel mundial se identificaron variantes de preocupación (VOC) y variantes de interés (VOI), que presentan características biológicas diferentes. El objetivo del trabajo es describir los linajes y variantes de SARS-CoV-2 circulantes en Córdoba mediante tres estrategias. Se implementaron 3 estrategias, a partir de muestras de RNA positivas para el virus (Cts<30): 1)-secuenciación de genoma completo (ONT-MinION): 203 muestras analizadas desde marzo 2020 a junio 2021; 2)-secuenciación de un fragmento genómico de la proteína S (Sanger): 54 muestras analizadas entre febrero y abril 2021 en viajeros provenientes del exterior; y 3)-PCR en tiempo real para detección de VOC (TaqMan™ SARS-CoV-2 Mutation Panel, Applied Biosystems): 816 muestras analizadas entre mayo y junio de 2021.       Los resultados fueron: 1)-circulación de siete linajes con mayor predominancia de B.1.1.33.3 (N3) (40,5%) y B.1.499 (38,8%), entre marzo 2020 y enero 2021; y circulación de 12 linajes con presencia de VOC [P.1 (Gamma, 28,4%), B.1.1.7 (Alpha, 6,9%)] y VOI [C.37 (Lambda, 20,6%), B.1.427 (Epsilon, 10,8%), P2 (Zeta, 2,9%), B.1.526 (Iota, 2%)], entre febrero y junio 2021; 2)-presencia de VOC Alpha (26,4%) y Gamma (17%), y muestras compatibles con las VOI Epsilon y Zeta (9,4%); 3)-presencia de VOC Gamma (56%) y Alpha (11%), y otras variantes no tipificables por esta metodología. Los resultados muestran circulación de diversos linajes de SARS-CoV-2 en Córdoba, que variaron su distribución a lo largo del tiempo, según las distintas introducciones ocurridas, el movimiento poblacional y las ventajas evolutivas de unos sobre otros. En marzo 2021 se realizaron las primeras detecciones de VOC en la provincia (Alpha y Gamma), siendo la variante Gamma la que circula mayoritariamente en la actualidad. Si bien la secuenciación del genoma completo es la técnica que mayor información brinda, las otras 2 estrategias implementadas fueron y son de gran utilidad para la vigilancia epidemiológica molecular, favoreciendo la obtención de información en tiempo real. La estrategia 3 resulta una herramienta más simple, rápida y con mayor capacidad operativa para el screening molecular de VOC.

Amniotic fluid deficiency and congenital abnormalities both influence fluctuating asymmetry in developing limbs of human deceased fetuses

Fluctuating asymmetry (FA), as an indirect measure of developmental instability (DI), has been intensively studied for associations with stress and fitness. Patterns, however, appear heterogeneous and the underlying causes remain largely unknown. One aspect that has received relatively little attention in the literature is the consequence of direct mechanical effects on asymmetries. The crucial prerequisite for FA to reflect DI is that environmental conditions on both sides should be identical. This condition may be violated during early human development if amniotic fluid volume is deficient, as the resulting mechanical pressures may increase asymmetries. Indeed, we showed that limb bones of deceased human fetuses exhibited increased asymmetry, when there was not sufficient amniotic fluid (and, thus, space) in the uterine cavity. As amniotic fluid deficiency is known to cause substantial asymmetries and abnormal limb development, these subtle asymmetries are probably at least in part caused by the mechanical pressures. On the other hand, deficiencies in amniotic fluid volume are known to be associated with other congenital abnormalities that may disturb DI. More specifically, urogenital abnormalities can directly affect/reduce amniotic fluid volume. We disentangled the direct mechanical effects on FA from the indirect effects of urogenital abnormalities, the latter presumably representing DI. We discovered that both factors contributed significantly to the increase in FA. However, the direct mechanical effect of uterine pressure, albeit statistically significant, appeared less important than the effects of urogenital abnormalities, with an effect size only two-third as large. We, thus, conclude that correcting for the relevant direct factors allowed for a representative test of the association between DI and stress, and confirmed that fetuses form a suitable model system to increase our understanding in patterns of FA and symmetry development.Research Fund of the University of Antwerp, mobility grant from the Research Foundation – Flanders (FWO)

Food supplements increase adult tarsus length, but not growth rate, in an island population of house sparrows (Passer domesticus)

<p>Abstract</p> <p>Background</p> <p>Variation in food supply during early development can influence growth rate and body size in many species. However, whilst the detrimental effects of food restriction have often been studied in natural populations, how young individuals respond to an artificial increase in food supply is rarely investigated. Here, we investigated both the short-term and long-term effects of providing house sparrow chicks with food supplements during a key period of growth and development and assessed whether providing food supplements had any persistent effect upon adult size (measured here as tarsus length).</p> <p>Results</p> <p>Male nestlings tended to reach higher mass asymptotes than females. Furthermore, brood size was negatively associated with a chick's asymptotic mass. However, providing food supplements had no influence upon the growth rate or the asymptotic mass of chicks. Adults that received food supplements as chicks were larger, in terms of their tarsus length, than adults that did not receive extra food as chicks. In addition, the variation in tarsus length amongst adult males that were given food supplements as chicks was significantly less than the variance observed amongst males that did not receive food supplements.</p> <p>Conclusions</p> <p>Our results demonstrate that the food supply chicks experience during a critical developmental period can have a permanent effect upon their adult phenotype. Furthermore, providing extra food to chicks resulted in sex-biased variance in a size-related trait amongst adults, which shows that the degree of sexual size dimorphism can be affected by the environment experienced during growth.</p

The Effect of Genetic and Environmental Variation on Genital Size in Male Drosophila: Canalized but Developmentally Unstable

The genitalia of most male arthropods scale hypoallometrically with body size, that is they are more or less the same size across large and small individuals in a population. Such scaling is expected to arise when genital traits show less variation than somatic traits in response to factors that generate size variation among individuals in a population. Nevertheless, there have been few studies directly examining the relative sensitivity of genital and somatic traits to factors that affect their size. Such studies are key to understanding genital evolution and the evolution of morphological scaling relationships more generally. Previous studies indicate that the size of genital traits in male Drosophila melanogaster show a relatively low response to variation in environmental factors that affect trait size. Here we show that the size of genital traits in male fruit flies also exhibit a relatively low response to variation in genetic factors that affect trait size. Importantly, however, this low response is only to genetic factors that affect body and organ size systemically, not those that affect organ size autonomously. Further, we show that the genital traits do not show low levels of developmental instability, which is the response to stochastic developmental errors that also influence organ size autonomously. We discuss these results in the context of current hypotheses on the proximate and ultimate mechanisms that generate genital hypoallometry

Growth and Asymmetry of Soil Microfungal Colonies from “Evolution Canyon,” Lower Nahal Oren, Mount Carmel, Israel

Fluctuating asymmetry is a contentious indicator of stress in populations of animals and plants. Nevertheless, it is a measure of developmental noise, typically obtained by measuring asymmetry across an individual organism's left-right axis of symmetry. These individual, signed asymmetries are symmetrically distributed around a mean of zero. Fluctuating asymmetry, however, has rarely been studied in microorganisms, and never in fungi.We examined colony growth and random phenotypic variation of five soil microfungal species isolated from the opposing slopes of “Evolution Canyon,” Mount Carmel, Israel. This canyon provides an opportunity to study diverse taxa inhabiting a single microsite, under different kinds and intensities of abiotic and biotic stress. The south-facing “African” slope of “Evolution Canyon” is xeric, warm, and tropical. It is only 200 m, on average, from the north-facing “European” slope, which is mesic, cool, and temperate. Five fungal species inhabiting both the south-facing “African” slope, and the north-facing “European” slope of the canyon were grown under controlled laboratory conditions, where we measured the fluctuating radial asymmetry and sizes of their colonies. from the “African” slope were more asymmetric than those from the “European” slope.Our study suggests that fluctuating radial asymmetry has potential as an indicator of random phenotypic variation and stress in soil microfungi. Interaction of slope and species for both growth rate and asymmetry of microfungi in a common environment is evidence of genetic differences between the “African” and “European” slopes of “Evolution Canyon.

Proteomics of Buccal Cavity Mucus in Female Tilapia Fish (Oreochromis spp.): A Comparison between Parental and Non-Parental Fish

Mouthbrooding is an elaborate form of parental care displayed by many teleost species. While the direct benefits of mouthbrooding such as protection and transportation of offsprings are known, it is unclear if mouthbrooding offers additional benefits to embryos during incubation. In addition, mouthbrooding could incur negative costs on parental fish, due to limited feeding opportunities. Parental tilapia fish (Oreochromis spp.) display an elaborated form of parental care by incubating newly hatched embryos in oral buccal cavity until the complete adsorption of yolk sac. In order to understand the functional aspects of mouthbrooding, we undertake a proteomics approach to compare oral mucus sampled from mouthbrooders and non-mouthbrooders, respectively. Majority of the identified proteins have also been previously identified in other biological fluids or mucus-rich organs in different organisms. We also showed the upregulation of 22 proteins and down regulation of 3 proteins in mucus collected from mouthbrooders. Anterior gradient protein, hemoglobin beta-A chain and alpha-2 globin levels were lower in mouthbrooder samples. Mouthbrooder oral mucus collectively showed increase levels of proteins related to cytoskeletal properties, glycolytic pathway and mediation of oxidative stress. Overall the findings suggest cellular stress response, probably to support production of mucus during mouthbrooding phase

Leaf Morphology, Taxonomy and Geometric Morphometrics: A Simplified Protocol for Beginners

Taxonomy relies greatly on morphology to discriminate groups. Computerized geometric morphometric methods for quantitative shape analysis measure, test and visualize differences in form in a highly effective, reproducible, accurate and statistically powerful way. Plant leaves are commonly used in taxonomic analyses and are particularly suitable to landmark based geometric morphometrics. However, botanists do not yet seem to have taken advantage of this set of methods in their studies as much as zoologists have done. Using free software and an example dataset from two geographical populations of sessile oak leaves, we describe in detailed but simple terms how to: a) compute size and shape variables using Procrustes methods; b) test measurement error and the main levels of variation (population and trees) using a hierachical design; c) estimate the accuracy of group discrimination; d) repeat this estimate after controlling for the effect of size differences on shape (i.e., allometry). Measurement error was completely negligible; individual variation in leaf morphology was large and differences between trees were generally bigger than within trees; differences between the two geographic populations were small in both size and shape; despite a weak allometric trend, controlling for the effect of size on shape slighly increased discrimination accuracy. Procrustes based methods for the analysis of landmarks were highly efficient in measuring the hierarchical structure of differences in leaves and in revealing very small-scale variation. In taxonomy and many other fields of botany and biology, the application of geometric morphometrics contributes to increase scientific rigour in the description of important aspects of the phenotypic dimension of biodiversity. Easy to follow but detailed step by step example studies can promote a more extensive use of these numerical methods, as they provide an introduction to the discipline which, for many biologists, is less intimidating than the often inaccessible specialistic literature