Phenotypic Variation Research Articles

Predictable ecological dynamics over incredibly small spatial scales influence early-life phenotypes in a species with temperature-dependent sex determination.

Phenotype-environment associations in neonatal animals may arise in wild environments by virtue of ecological dynamics within the nest. Such dynamics may be of special importance to the evolution of temperature-dependent sex determination (TSD), an enigmatic trait which can be adaptive when the incubation temperatures that affect sexual differentiation also have differential effects on fitness of the sexes. To infer causal effects of the nest environment on fitness-relevant phenotypes, we apply structural equation modeling (SEM) to a 14-year dataset of 3085 individual embryos whose position in 179 wild snapping turtle nests could be estimated. We find that temperature has a positive effect on hatchling size, and that the same temperatures that predict hatchling size also predict sex of hatchlings. Further, the probability that embryos develop as males is correlated with hatchling size in the wild, where across all environments, males are slightly and significantly larger than females at hatching. Our SEM reveals that the covariance between size and sex arises because of temperature effects on size, and because of a predictable covariance between egg placement within the nest coupled with maternal effects on egg size. Finally, embryos deep in the nest have a high probability of becoming male even in the hottest years. Our study suggests ecological dynamics occurring within the nest are an interesting and underappreciated source of phenotypic variation. Our study also supports the view that TSD is an adaptive trait, rather than a neutral trait, by showing consistent associations between phenotype and temperature in wild nests of a TSD reptile.

Linking phenotypic variation to patterns of genetic isolation along a speciation continuum.

Investigating taxa at varying stages of divergence can shed light on the evolutionary forces that lead to reproductive isolation and eventual speciation. The forces promoting isolation vary in space and time, which makes it difficult to reconstruct the trajectory that resulted in the divergence observed among species today. The red macroalgal genus Plocamium is known worldwide for its cryptic genetic and chemical diversity. Previous work on the genus Plocamium in Antarctica observed two haplotypes along the western Antarctic Peninsula that have been treated as the same species. Using 10 microsatellite loci, we observed that these two haplotypes correspond to two highly divergent, co-occurring genetic entities in Antarctic Plocamium, which are located within close vicinity of each other at the same sites. The morphology of the reproductive structures, a feature commonly used to identify cryptic species in Plocamium, as well as the timing of reproduction, differed significantly between the two genetic entities. Altogether, this suggests that two Antarctic Plocamium species exist on the western Antarctic Peninsula. We observed evidence for high levels of selfing in both genetic entities, which likely exacerbated the lack of gene flow between them. In addition, we identified concomitant chemodiversity that generates compelling evidence of early evolutionary divergence within one of these entities. This chemodiversity has ecological consequences for its main grazer, which alludes to one putative evolutionary driver of divergence. Antarctic Plocamium spp. provide a promising model system for investigating the eco-evolutionary forces that initiate and maintain species boundaries.

Genotype, Environment and Heavy Metals: Variability of The Content of Elements in 40 Potato Varieties from Central-Eastern Poland.

This study investigates the accumulation of toxic heavy metals-cadmium (Cd), chromium (Cr), cobalt (Co), nickel (Ni), lead (Pb), and strontium (Sr)-in potato tubers grown under diverse meteorological and soil conditions in east-central Poland. Conducted from 2021 to 2023 at the Variety Assessment Experimental Station in Uhnin on light acidic soil, the field experiment employed a randomized block design with 3 replications. Forty potato cultivars of varying maturity were evaluated, with agronomic practices adhering to GAP and uniform fertilization applied. Potato tubers were exposed to thermal neutron flux for 2 hours. Gamma radiation detection was conducted using a high-purity germanium (HPGe) detector cooled with liquid nitrogen to enhance resolution. The study highlights significant phenotypic variability in heavy metal accumulation, influenced by genetic, environmental, and genotype × environment interaction factors. Results showed substantial effects of cultivar, year, and their interactions, with varieties (V) accounting for 8.7-36.2% of the variance, environmental factors (Y) contributing 41.2-82.2%, and genotype × environment interactions (V × Y) ranging from 5.5-46.7%. Year-to-year variability was most pronounced for lead, while nickel showed the least variability. Soil pH and humus played a key role in shaping the bioavailability and accumulation of metals in potato tubers.

Identification of a germline deep intronic PTEN-deletion leading to exonization through whole genome and targeted RNA sequencing.

PTEN Hamartoma Tumor Syndrome (PHTS) is an autosomal dominant disorder characterized by high penetrance and significant phenotypic variability. In most patients, targeted high-throughput sequencing (HTS) approaches enable the detection of loss-of-function pathogenic variants in PTEN, a tumor suppressor gene acting as a negative regulator of the PI3K-AKT pathway. We describe a patient exhibiting a clinical phenotype strongly indicative of PHTS, yet lacking a molecular diagnosis through PTEN-targeted HTS. After several years of diagnostic uncertainty, trio whole genome sequencing (WGS) ultimately identified a de novo germline deep intronic 98bp deletion in PTEN intron 5 (c.492 + 1671_492 + 1768del). Targeted RNA sequencing revealed the inclusion of a pseudoexon, resulting in a frameshift and predicted protein truncation at codon 171 (p.Val166Asnfs*6). These data underline the importance of WGS approaches in detecting deep intronic structural variants, that may be overlooked by conventional methods.

Colourful network: pair-bonding temporal dynamics involve sexual signals and impact reproduction

Abstract Mate choice and pair-bonding are the products of complex decisions involving repeated social interactions over time. They generally rely on multiple sexual signals and behaviours, depend on the phenotype and experiences of the chooser and are affected by environmental conditions and competition for mate access. However, studies investigating the mechanisms of mate selection often ignore the dynamic aspects of the pair formation. In the current study, we used social network analyses to (1) describe sexual interactions over time in multiple groups of captive zebra finches (Taeniopygia guttata), (2) ask how individual sexual signals and body condition relate to pair-bonding temporal dynamics and (3) investigate whether sexual networks influence assortative mating and reproductive performance. We followed sexual interactions of 8 sex-balanced groups of 8 individuals to extract social network metrics over 8 sessions of observation. We assessed individual body condition, sexual signals and couples’ pairing latency, laying date, clutch size and embryo viability. Pair-bonding dynamics were first characterized by song interactions between most individuals, then by numerous allopreening and clumping behaviours, targeting more specific partners. More colourful individuals became engaged in more sexual interactions more rapidly, and such network dynamics explained assortative mating for beak colour. Interestingly, being involved in song interactions was negatively associated with reproductive performances while the reverse was true for being involved in allopreening and clumping interactions. Our study highlights the need to study pair-bonding dynamics to better understand how variations in individual phenotype within sexual networks explain assortative mating and reproductive performance in monogamous species.

Production Location Affects Tuber Shape Phenotype of Late-Season Russet Selections and Cultivars from the Northwest Potato Variety Development Program (NWPVDP)

Abstract Potato tuber length-to-width ratio (L/W) is an important trait for consumer visual acceptance, pack-out efficiency, French fry production, and waste recovery. In the U.S. Northwest Potato Variety Development Program (NWPVDP), L/W accounts for 13% of the overall postharvest score. Selections with L/W ≥ 1.8 are preferred for maximum raw-product recovery (≥ 7.6-cm-long fries). However, tuber shape often depends on production location. Our objectives were to (1) model the effects of production location on L/W using 26 years of historical data from the NWPVDP, and (2) quantify the variability in tuber shape phenotype of selected NWPVDP varieties across production locations (WA, ID, OR). A mixed linear model demonstrated that tuber L/W was strongly affected by location, year, and location-by-year interactions (40% of total variation), while variety and variety-by-location accounted for 43% of total variation. L/W of the 227-284-g tubers of twenty-two released varieties from the NWPVDP averaged 1.65, 1.70, and 1.92 for WA, OR, and ID, respectively, and ranged from a low of 1.51 and 1.53 (cvs. Payette Russet & Palisade Russet) to a high of 2.06 and 2.12 (cvs. Ranger Russet & Echo Russet) across locations. The round phenotype of Palisade was stable across locations, leading to consistently low fry recovery (84% FW). By contrast, Payette tubers were invariably round in WA and OR, but elongated when grown in ID. The elongated phenotypes of Echo and Ranger from all locations ensured maximum fry recovery (94 to 95% FW), despite the relatively high variation in L/W (9–13%) attributable to location. Collectively, our results suggest an opportunity for genetic selection of L/W that are stable across locations for market specific reductions in shape waste. Future work should focus on identifying key mechanisms which are impacted by production environment for improved stability of L/W. Furthermore, cultural management strategies should be optimized for L/W consistency and usability by all sectors of the potato industry.

DNA-binding affinity and specificity determine the phenotypic diversity in BCL11B-related disorders.

BCL11B is a Cys2-His2 zinc-finger (C2H2-ZnF) domain-containing, DNA-binding, transcription factor with established roles in the development of various organs and tissues, primarily the immune and nervous systems. BCL11B germline variants have been associated with a variety of developmental syndromes. However, genotype-phenotype correlations along with pathophysiologic mechanisms of selected variants mostly remain elusive. To dissect these, we performed genotype-phenotype correlations of 92 affected individuals harboring a pathogenic or likely pathogenic BCL11B variant, followed by immune phenotyping, analysis of chromatin immunoprecipitation DNA-sequencing data, dual-luciferase reporter assays, and molecular modeling. These integrative analyses enabled us to define three clinical subtypes of BCL11B-related disorders. It is likely that gene-disruptive BCL11B variants and missense variants affecting zinc-binding cysteine and histidine residues cause mild to moderate neurodevelopmental delay with increased propensity for behavioral and dental anomalies, allergies and asthma, and reduced type 2 innate lymphoid cells. Missense variants within C2H2-ZnF DNA-contacting α helices cause highly variable clinical presentations ranging from multisystem anomalies with demise in the first years of life to late-onset, hyperkinetic movement disorder with poor fine motor skills. Those not in direct DNA contact cause a milder phenotype through reduced, target-specific transcriptional activity. However, missense variants affecting C2H2-ZnFs, DNA binding, and "specificity residues" impair BCL11B transcriptional activity in a target-specific, dominant-negative manner along with aberrant regulation of alternative DNA targets, resulting in more severe and unpredictable clinical outcomes. Taken together, we suggest that the phenotypic severity and variability is largely dependent on the DNA-binding affinity and specificity of altered BCL11B proteins.

Genetic parameters and parental and early-life effects of boar semen traits

BackgroundThe objectives of this study were to estimate genetic parameters and studying the influence of early-life and parental factors on the semen traits of boars. The dataset included measurements on 449,966 ejaculates evaluated using a Computer-Assisted Sperm Analysis (CASA) system from 5692 artificial insemination (AI) boars. In total, we considered 16 semen traits measured on fresh semen and 6 sperm motility traits measured on semen after storage. Early-life effects included the dam’s parity, ages of the dam and sire, gestation length, litter size, litter sex ratio, number of piglets born alive, number of litter mates at weaning, rearing length, and weight gain. A repeatability model accounting for effects at collection was used to (1) estimate heritabilities and repeatabilities for semen traits and genetic and phenotypic correlations between traits, (2) test the significance of early-life effects, (3) quantify the contribution of exclusive dam and sire inheritances to the phenotypic variation, i.e., mitochondrial DNA and the Y chromosome, identified using a pedigree-based approach, and (4) quantify the contribution of maternal and paternal environment effects to the phenotypic variation of semen traits.ResultsWe reported heritabilities between 0.11 and 0.27 and repeatabilities between 0.20 and 0.65 for semen traits. Semen quality traits showed a skewed distribution, and their transformation significantly reduced their repeatability estimates. Motility traits measured after storage were genetically different from motility traits measured on fresh semen. Early-life had suggestive effects on a limited number of semen traits. Mitochondrial DNA and the Y chromosome did not explain a discerning proportion of the phenotypic variance and the effect of the paternal environment was also negligible. We estimated a significant maternal environment effect predominantly on sperm motility traits, explaining between 2.3 and 4.6% of the phenotypic variance. Including maternal environmental effects in the model reduced heritability estimates for sperm motility traits and total morphological abnormalities.ConclusionsOur findings indicate that trait transformation has a large effect on repeatability estimates of semen traits. Sperm motility traits measured on fresh semen are genetically different from sperm motility traits measured after storage. Early-life conditions can have an effect on later semen quantity and quality traits. Mitochondrial DNA and Y chromosome inheritances showed no effect on semen traits. Finally, we emphasize the importance of considering maternal effects when analysing semen traits, which results in lower heritability estimates.

Sepsis subphenotypes: bridging the gaps in sepsis treatment strategies

Sepsis, a heterogeneous illness produced by a dysregulated host response to infection, remains a severe mortality risk. Recent discoveries in sepsis research have stressed phenotyping as a feasible strategy for tackling heterogeneity and enhancing therapy precision. Sepsis phenotyping has moved from traditional stratifications based on severity and prognosis to dynamic, phenotype-driven therapeutic options. This review covers recent progress in connecting sepsis subgroups to personalized treatments, with a focus on phenotype-based therapeutic predictions and decision-support systems. Despite ongoing challenges, such as standardizing phenotyping frameworks and incorporating findings into clinical practice, this topic has enormous promise. By investigating phenotypic variation in therapy responses, we hope to uncover new biomarkers and phenotype-driven therapeutic solutions, laying the groundwork for more effective therapies and, ultimately improving patient outcomes.

Digest: Clinal variation in plant traits is shaped by plastic and evolutionary responses to water regimes and herbivory.

How do water regime and herbivory shape phenotypic variation in plants along environmental gradients? Using a multifactorial field common garden approach, Jameel et al. (2024) showed that water availability and herbivore abundance influence the expression of foliar and reproductive traits in the perennial forb Boechera stricta. The concordance between phenotypic plasticity, phenotypic clines, and the direction of selection demonstrates the adaptive nature of plasticity in ecologically relevant traits. Furthermore, the experimental manipulations highlight which agents of selection drive the evolution of these traits.

ГЕНЕТИЧЕСКАЯ ДЕТЕРМИНАЦИЯ НАКОПЛЕНИЯ МЕДИ В МИОКАРДЕ У КРУПНОГО РОГАТОГО СКОТА ЗАПАДНОЙ СИБИРИ

The purpose of the study is to assess the hereditary nature of copper accumulation in the heart muscle of Holstein bulls bred in the ecological and climatic conditions of Western Siberia. The results of assessing the level of copper in the myocardium of Holstein bulls aged 12–13 months, which are the descendants of 4 sires, are presented. Blood was taken from animals with a live weight of 330–365 kg, bred in a large livestock enterprise located in Western Siberia. The level of copper in the myocardium of bulls was determined by atomic absorption spectrometry with flame and electrothermal atomization. One-way analysis of variance was used to determine differences between groups. η2 was used as a test to assess the effect size, and Tukey’s test was used for post hoc comparisons. It was found that the average copper content in the myocardium of Holstein bulls was 3.24 ± 0.04 mg/kg. Phenotypic variability of copper concentration in the heart muscle was characterized by low values. The established differences (p-value < 0.05) in copper content in the offspring of different sires reflect the genetic determination of the accumulation of this metal in the heart muscle. The strength of influence of the factor of paternal affiliation of bulls on the level of copper content in the myocardium was 35 %. The level of copper in the myocardium was higher by 0.52 mg/kg in the offspring of the bull Fabio compared to the sons of Brio. The reference interval for myocardial copper content based on the central 95 % percentile with 90 % confidence intervals was 2.9 (2.78 – 3.02) – 3.7 (3.57–3.82) mg/kg.

НАСЛЕДУЕМОСТЬ ПРОДОЛЖИТЕЛЬНОСТИ ВЕГЕТАЦИОННОГО ПЕРИОДА ГИБРИДАМИ F2 ЧЕЧЕВИЦЫ В УСЛОВИЯХ ОМСКОЙ ОБЛАСТИ

The purpose of research is to identify the spectrum of genetic diversity of early ripening in hybrid combinations of the second generation of lentils to accelerate the selection of valuable genotypes and create varieties adapted to the climatic conditions of the region. Research was carried out from 2020 to 2022 at the experimental site of the educational and experimental farm of the Federal State Budgetary Educational Institution of Higher Education Omsk Civil Aviation in the southern forest-steppe of the Omsk Region. The value of the hydrothermal coefficient indicates very dry conditions in 2020 (HTC = 0.62) and 2021 (HTC = 0.68), slightly dry conditions in 2022 (HTC = 1.02). The soil of the experimental plot is medium-deep meadow-chernozemic (45 cm), low-humus (3.95 % humus), medium-loamy (35 % physical clay) with a soil solution reaction close to neutral (pH – 6.5). The predecessor is spring soft wheat. Four collection samples of lentils with a complex of economically valuable traits of different ecological and geographical origin were subject to study: k-2888 (Moldova), k-2849 (Russia, Altai Region), Rauza (Russia, Oryol Region), Vehovskaya (Russia, Saratov Region) – and four F2 hybrids obtained as a result of intraspecific crossing: k-2888 × Rauza, k-2888 × Vehovskaya, k-2849 × Rauza, k-2849 × Vehovskaya. Analysis of the data obtained showed that the duration of the growing season is characterized by low heredity (H2 = 19.0 %). This means that the phenotypic variability of the trait is determined by the natural and climatic conditions of the environment. It is advisable to select valuable early ripening genotypes in later generations of hybrids under favorable conditions. Hybrid combinations that are promising in practical selection of lentils for early ripening are: k-2849 × Vehovskaya and k-2888 × Vehovskaya.

Unravelling the Mexican Magnolia dealbata (Magnoliaceae) species complex

In the last two decades, approximately 80 new Magnolia species have been described from the Neotropics; thus this region now hosts almost half of the world’s known Magnolia diversity. Many of these likely are not segregate taxa but rather separate populations or groups of populations of the previously broadly circumscribed, widespread species. Such is possibly the case of the Magnolia dealbata species complex (belonging to Magnolia sect. Macrophylla), distributed throughout the Sierra Madre Oriental mountain range in Eastern Mexico. This species complex has been divided into six morphospecies based on morphological criteria only. However, recent microsatellite markers have suggested that these may be a single entity. Considering geographical data and the isolation of populations, we hypothesised that the different morphospecies could form two entities, corresponding to the north and centre of the Sierra Madre Oriental. This hypothesis was tested by morphological observations, chloroplast comparisons and phylogenetic analyses of plastomes, angiosperm DNA plastid barcodes and Magnolia-specific plastid DNA barcodes from hypervariable regions. Phylogenetic results from plastomes and angiosperm DNA plastid barcodes refute the multispecies hypothesis and show that the six morphospecies of this complex inhabiting the Sierra Madre Oriental form a single entity. Evidence is also provided that the morphological characters used to delimit the morphospecies of the complex, mainly numbers of carpels and the absence-presence and colour of a spot in the petals, are, in fact, phenotypic variation and have no taxonomic significance. Therefore, the taxa M. alejandrae, M. nuevoleonensis, M. rzedowskiana, M. vovidesii and M. zotictla are synonymised here under M. dealbata. However, the possibility remains of including the latter as a variety of M. macrophylla, based on the results of the Magnolia-specific plastid DNA barcodes. Furthermore, this study proposes an updated conservation status for M. dealbata, highlighting the urgent need for effective conservation measures. The taxonomic clarification presented here is essential to properly target such efforts, especially in the face of threats such as indiscriminate collection and vulnerability to environmental disturbance.

QTL mapping of Fusarium ear rot resistance using genotyping by target sequencing (GBTS) in maize.

Fusarium ear rot (FER) is a global disease caused by the fungal pathogen Fusarium verticillioides. Maize FER resistance is a quantitative trait controlled by polygenes. In this study, a doubled haploid (DH) population involving 159 lines, developed from the inbred lines B73 (susceptible) and CXS161 (highly resistant), was inoculated with Fusarium verticillioides across 4-year-location environment combinations in China during 2021 and 2022. The lines were genotyped using target sequencing with a 10K SNP array. The results showed that the estimated broad-sense heritability (H2) in each environment ranged from 0.659 to 0.871, with an overall H2 of 0.805. The average genetic length between adjacent markers in the genetic map constructed using multiple single-nucleotide polymorphisms (mSNP) was smaller than that constructed using SNP, whereas the maximal genetic length was almost the same. Using a genetic map constructed with a SNP, two quantitative trait loci (QTL) were identified on chromosomes 2 and 5, which explained 7.65% and 9.58% of the phenotypic variation, respectively. Using the genetic map constructed by mSNP, four QTL were identified, explaining 6.04-12.60% of the phenotypic variation. Moreover, two kompetitive allele-specific PCR (KASP) markers were developed using single-marker analysis methods, with one KASP marker validated across a backcross population that can be effectively used to identify FER resistance. In conclusion, using mSNP for genetic map construction does not confer advantages when the population size is limited and the marker density is high. However, the mSNP-constructed map identified more minor-effectQTL despite possessing a lower likelihood of the odds (LOD) values.

Deep resequencing unveils novel SNPs, InDels, and large structural variants for the clonal fingerprinting of sweet orange [Citrus sinensis (L.) Osbeck

The large phenotypic variability characterizing the sweet orange [Citrus sinensis (L.) Osbeck] germplasm arose from spontaneous somatic mutations and led to the diversification of major groups (common, acidless, Navel, and pigmented). Substantial divergence also occurred within each varietal group. The genetic basis of such variability (i.e., ripening time, fruit shape, color, acidity, and sugar content) is largely uncharacterized, and therefore not exploitable for molecular breeding. Moreover, the clonal nature of all sweet orange accessions hinders the traceability of propagation material and fruit juice using low-density molecular markers. To build a catalog of somatic mutations in Italian varieties, 20 accessions were sequenced at high coverage. This allowed the identification of single nucleotide polymorphisms (SNPs), structural variants (SVs), and large hemizygous deletions, specific to clones or varietal groups. A panel of 239 SNPs was successfully used for genotyping 221 sweet orange accessions, allowing them to be clustered into varietal groups. Furthermore, genotyping of SNPs and SVs was extended to leaf and juice samples of commercial varieties belonging to two varietal groups (Moro and Tarocco) collected from 26 sites in Southern Italy, confirming the usefulness of the identified markers for the identification of specific clones. Interestingly, we found that the insertion of the transposable element VANDAL in the gene exons significantly affected the level of allelic-specific expression. Finally, the markers developed in the present work contribute to unraveling the origin and diversification of sweet oranges, representing a reliable and efficient molecular tool for the unambiguous fingerprint of somatic mutants and an asset for the traceability of orange plant material and fruit juice.

Field Assessment of Turkish fir (Abies bornmuelleriana) Resistance to Five Root-Rotting Phytophthora Species.

Turkish fir (Abies bornmuelleriana) has been evaluated as a Phytophthora Root Rot (PRR)-resistant alternative to other PRR-susceptible Abies Christmas tree species. Though Turkish fir survival under heavy PRR disease pressure exceeds that of other host species, previous research has suggested that there may be variability in resistance owing to pedigree, ambient environment, and Phytophthora species. To assess differences in PRR survival in the field, 36 open-pollinated families of Turkish fir were challenged with a mixture of five species of Phytophthora under conditions conducive for disease. Seedlings were grown from seed that was gathered during a provenance collection effort from three provinces in Turkey. At the collection locations in each province, mother trees were located along an altitudinal gradient. The goals for this study included determining Turkish fir resistance in comparison to susceptible fir spp., evaluating phenotype among Turkish fir families, assessing if differences in phenotypes could be attributable to source location or elevation, determining if source province or elevation influenced mortality, and comparing recovery of the five Phytophthora spp. used as inoculum. Turkish fir was demonstrated to be more resistant than noble fir (A. procera) or Fraser fir (A. fraseri) under the experimental conditions. Among the 36 Turkish fir families, six families had a significantly lower probability of PRR mortality compared to all other families; half of these families were from the Karabük province. Similarly, the Karabük province had the lowest overall mortality when family mortality proportions were totaled and compared among provinces. Evaluation of mortality among families from higher elevation sites within a province showed reduced mortality in comparison to mid and lower elevation sites, with variation among seed sources from different provinces. Among the five species of Phytophthora bulked for inoculum, P. cryptogea was the predominant species recovered from dead seedlings in both years. Results suggest that Turkish fir may be a viable PRR-resistant option for utilization in the Christmas tree industry despite some variability in phenotype among family.

Species evolution: cryptic species and phenotypic noise with a particular focus on fungal systematics

The evolution of a species can be understood in the context of two major concepts—the cryptic species concept and the phenotypic noise concept. The former represents morphologically indistinguishable but genetically distinct evolutionary lineages, while the latter represents the phenotypic variations of an isogenic population. Although the concept of cryptic species currently represents a general topic, its effect on other aspects of biology, such as biodiversity, ecology, evolutionary biology, and taxonomy, is still unclear. In particular, cryptic species cause complications and prevent the development of a clear taxonomy. The phenotypic noise concept or phenotypic plasticity generally refers to the various expressions of phenotypes in different environments. Hence, the cryptic species concept refers to genetic variations, while the phenotypic noises concept is about non-genetic variations. Although both concepts are opposites, they each contribute significantly to the evolutionary process of an organism. Despite the extensive research studies and publications discussing those two concepts in separate accounts, a concise account that combines and compares both concepts are generally lacking. Nevertheless, these are essential to understand the evolutionary process clearly. This review addresses the available literature on this topic, intending to provide a general and overall discussion on both the cryptic species concept and the phenotypic noise concept and their effect on evolution, ecology, biodiversity, and taxonomy with a special focus on fungal systematics. hence, several fungal case studies representing the two concepts are presented, compared, and discussed for a better understanding.

Genotype-Phenotype Spectrum of eyeGENE Patients With Familial Exudative Vitreoretinopathy: Novel Variants in Norrin/β-Catenin Signaling Pathway Genes.

To report the variants and genotype-phenotype correlations in patients with familial exudative vitreoretinopathy (FEVR) included in the eyeGENE database. A retrospective study was conducted in a cohort of 122 eyeGENE patients from 114 families with FEVR. Clinical details and genetic test results were provided by referring clinicians and clinical laboratories in the eyeGENE network, respectively. Genotype and phenotype information was reviewed, and reported variants were reclassified. Genetic test reports of 50 probands revealed 52 variants in the four genes of the Norrin/β-catenin signaling pathway: LRP5, FZD4, TSPAN12, and NDP. Following variant reclassification, 35 of the reported variants were interpreted as pathogenic or likely pathogenic (12 in LRP5, 11 in FZD4, seven in TSPAN12 and five in NDP), providing a conclusive test result for nearly one-third (32%) of the probands. Among the reported variants, 18 were novel (34.6%) and two-thirds were missense. Retinal detachment was reported less in patients with variants in TSPAN12 (P = 0.017). One-third of the patients (33.3%) with an FZD4 variant had asymmetric findings. In contrast, asymmetry was less pronounced in patients with variants in TSPAN12 (11.1%). This was one of the largest cohorts reviewed from North America, expanding the variant spectrum in FEVR. Among the eyeGENE FEVR patients, disease-associated variants in Norrin/β-catenin signaling pathway genes can explain one-third of the cohort. LRP5 and FZD4 variants were the most common. The genotype-phenotype correlations supported the phenotypic variability in FEVR.

EMT-driven plasticity prospectively increases cell–cell variability to promote therapeutic adaptation in breast cancer

Cellular plasticity enables cancer cells to adapt non-genetically, thereby preventing therapeutic success. The epithelial-mesenchymal transition (EMT) is a type of plasticity linked to resistance and metastasis. However, its exact impact on population diversity and its dynamics under chemotherapy is unknown. We used single-cell transcriptomics to investigate phenotypic diversity dynamics upon treatment in two in vitro models of triple negative breast cancer (TNBC), where EMT-driven plasticity is either induced or spontaneously occurring. We report that EMT-driven plasticity confers higher phenotypic cell–cell variability (p < 0.001) while enriching for stem-like cells. Genetic and phenotypic cell–cell variability were not consistently correlated. High-plasticity populations displayed more pre-adapted cells before treatment (p = 0.03). In a population displaying spontaneous EMT and phenotypic variation, pre-adapted cells were a rare minority of high-scoring outliers whose expression patterns correlated with survival in TNBC patients subjected to chemotherapy (p = 0.03). Higher plasticity was not associated with a partial EMT status. Our results provide novel insights on how EMT-driven plasticity promotes a prospective diversification process increasing population phenotypic diversity, which can yield rare pre-adapted states before treatment. This highlights the need to tackle phenotypic diversity prior to treatment in high-plasticity tumours.

Characterization of microbiota signatures in Iberian pig strains using machine learning algorithms

BackgroundThere is a growing interest in uncovering the factors that shape microbiome composition due to its association with complex phenotypic traits in livestock. Host genetic variation is increasingly recognized as a major factor influencing the microbiome. The Iberian pig breed, known for its high-quality meat products, includes various strains with recognized genetic and phenotypic variability. However, despite the microbiome’s known impact on pigs’ productive phenotypes such as meat quality traits, comparative analyses of gut microbial composition across Iberian pig strains are lacking. This study aims to explore the gut microbiota of two Iberian pig strains, Entrepelado (n = 74) and Retinto (n = 63), and their reciprocal crosses (n = 100), using machine learning (ML) models to identify key microbial taxa relevant for distinguishing their genetic backgrounds, which holds potential application in the pig industry. Nine ML algorithms, including tree-based, kernel-based, probabilistic, and linear algorithms, were used.ResultsBeta diversity analysis on 16 S rRNA microbiome data revealed compositional divergence among genetic, age and batch groups. ML models exploring maternal, paternal and heterosis effects showed varying levels of classification performance, with the paternal effect scenario being the best, achieving a mean Area Under the ROC curve (AUROC) of 0.74 using the Catboost (CB) algorithm. However, the most genetically distant animals, the purebreds, were more easily discriminated using the ML models. The classification of the two Iberian strains reached the highest mean AUROC of 0.83 using Support Vector Machine (SVM) model. The most relevant genera in this classification performance were Acetitomaculum, Butyricicoccus and Limosilactobacillus. All of which exhibited a relevant differential abundance between purebred animals using a Bayesian linear model.ConclusionsThe study confirms variations in gut microbiota among Iberian pig strains and their crosses, influenced by genetic and non-genetic factors. ML models, particularly CB and RF, as well as SVM in certain scenarios, combined with a feature selection process, effectively classified genetic groups based on microbiome data and identified key microbial taxa. These taxa were linked to short-chain fatty acids production and lipid metabolism, suggesting microbial composition differences may contribute to variations in fat-related traits among Iberian genetic groups.