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Natural selection is believed to universally work to lower mutation rates (MR) due to the negative impact of mutations on individual fitness. Mutator alleles have only been found to be co-selected by genetic linkage with adaptive alleles in prokaryotes. Sexual reproduction substantially reduces genetic linkage, allowing selection to effectively eradicate mutator alleles. The current understanding, therefore, is that in sexually reproducing populations selection always works to lower MR, limited by the effective population size that determines the overall selection efficiency. In the present paper, we apply a Monte Carlo model of a sexually reproducing population and demonstrate that selection acting on MR does not universally favor lower MR but depends on the mode of selection acting on adaptive phenotypic traits. We demonstrate a unique previously unreported co-selective process that can drive the evolution of higher MR in sexually reproducing populations. Our results show that MR evolution is significantly influenced by multigenic inheritance of both MR and adaptive traits that are under selection. Our results also show that, contrary to the generally accepted axiom, population size appears not to affect the strength of selection uniformly but likely forms an intra-population gradient that generates a "biased sampling" process that has an opposite effect on selection strength and thus modulates or even negates the effect of population size on MR evolution. Based on our results, we propose an expanded population genetics theory of the evolution of mutation rates in sexually reproducing organisms. Our results have potential implications for understanding processes underlying rapid adaptive change in speciation and related macroevolutionary patterns.

Populations of chemotactic bacteria can rapidly expand into new territory by consuming and chasing an attractant cue in the environment, increasing the population’s overall growth in nutrient-rich environments. Although the migrating fronts driving this expansion contain cells of multiple swimming phenotypes, the consequences of non-genetic diversity for population expansion are unknown. Here, through theory and simulations, we predict that expanding populations non-genetically adapt their phenotype composition to migrate effectively through multiple physical environments. Swimming phenotypes in the migrating front are spatially sorted by chemotactic performance, but the mapping from phenotype to performance depends on the environment. Therefore, phenotypes that perform poorly localize to the back of the group, causing them to selectively fall behind. Over cell divisions, the group composition dynamically enriches for high-performers, enhancing migration speed and overall growth. Furthermore, non-genetic inheritance controls a trade-off between large composition shifts and slow responsiveness to new environments, enabling a diverse population to out-perform a non-diverse one in varying environments. These results demonstrate that phenotypic diversity and collective behavior can synergize to produce emergent functionalities. Non-genetic inheritance may generically enable bacterial populations to transiently adapt to new situations without mutations, emphasizing that genotype-to-phenotype mappings are dynamic and context-dependent.

Organisms continuously modify their living conditions via extended genetic effects on their environment, microbiome, and in some species culture. These effects can impact the fitness of current but also future conspecifics due to non-genetic transmission via ecological or cultural inheritance. In this case, selection on a gene with extended effects depends on the degree to which current and future genetic relatives are exposed to modified conditions. Here, we detail the selection gradient on a quantitative trait with extended effects in a patch-structured population, when gene flow between patches is limited and ecological inheritance within patches can be biased towards offspring. Such a situation is relevant to understand evolutionary driven changes in individual condition that can be preferentially transmitted from parent to offspring, such as cellular state, micro-environments (e.g., nests), pathogens, microbiome, or culture. Our analysis quantifies how the interaction between limited gene flow and biased ecological inheritance influences the joint evolutionary dynamics of traits together with the conditions they modify, helping understand adaptation via non-genetic modifications. As an illustration, we apply our analysis to a gene-culture coevolution scenario in which genetically-determined learning strategies coevolve with adaptive knowledge. In particular, we show that when social learning is synergistic, selection can favour strategies that generate remarkable levels of knowledge under intermediate levels of both vertical cultural transmission and limited dispersal. More broadly, our theory yields insights into the interplay between genetic and non-genetic inheritance, with implications for how organisms evolve to transform their environments.

OBJECTIVE Early life interindividual variation in hypothalamic-pituitary-adrenal (HPA) reactivity to stress is predictive of later life psychological and physical well-being, including the development of many pathological syndromes that are often sex-biased. A complex and interactive set of environmental and genetic causes for such variation has been implicated by previous studies, though little attention has been paid to nonadditive effects (e.g. dominance, X-linked) or sex-specific genetic effects. METHOD We used a large pedigreed sample of captive 3-4 months old infant rhesus macaques (N = 2,661, 54% female) to fit univariate and multivariate linear mixed quantitative genetic models for four longitudinal blood cortisol samples and three reliable ratings of infant temperament (nervousness, gentleness, confidence) during a mother-infant separation protocol. RESULTS Each trait had a moderate narrow-sense heritability (h², 0.26-0.46), but dominance effects caused the first two cortisol samples to have much larger broad-sense heritabilities (H², 0.57 and 0.77). We found no evidence for X-linked variance or common maternal environment variance. There was a sex difference in heritability of the first cortisol sample (hf² < hm²), suggesting differing genetic architecture of perception of maternal separation and relocation during infancy. Otherwise, genetic covariance matrices for the sexes were very similar. Genetic correlations between cortisol levels and temperament were weak (< |0.4|) but stronger than residual or phenotypic correlations. CONCLUSIONS HPA reactivity and temperament had a primarily additive genetic basis in infant macaques, but there were important complexities to the genetic architecture of including genetic dominance and sex differences in heritability at this early life stage. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

The histone modification H3K27me3 plays a central role in Polycomb-mediated epigenetic silencing. H3K27me3 recruits and allosterically activates Polycomb Repressive Complex 2 (PRC2), which adds this modification to nearby histones, providing a read/write mechanism for inheritance through DNA replication. However, for some PRC2 targets, a purely histone-based system for epigenetic inheritance may be insufficient. We address this issue at the Polycomb target FLOWERING LOCUS C (FLC) in Arabidopsis thaliana, as a narrow nucleation region of only ~three nucleosomes within FLC mediates epigenetic state switching and subsequent memory over many cell cycles. To explain the memory’s unexpected persistence, we introduce a mathematical model incorporating extra protein memory storage elements with positive feedback that persist at the locus through DNA replication, in addition to histone modifications. Our hybrid model explains many features of epigenetic switching/memory at FLC and encapsulates generic mechanisms that may be widely applicable.

The field of medical genetics is rapidly expanding. Genetics is becoming increasingly important in the general practice of medicine. Ideograms are schematic representations of banding patterns used by cytogeneticists to standardize numbering of specific bands. The older method, quinacrine banding, or Q-banding, produces the same dark and light patterns, but requires the use of a fluorescence microscope and is used routinely. However, mosaicism for many different autosomal trisomies, that is, the presence of both normal and trisomic cells in one individual, has been described in viable infants. In polygenic inheritance, multiple genetic influences in combination act together to produce a disorder. In multifactorial disorders, there is no evidence to suggest simple Mendelian inheritance. Genetic counseling involves the explanation of the manifestations of the disorder, the natural history and treatment, the inheritance pattern, the risks of recurrence, and the methods of prenatal and postnatal diagnosis.

Primary ciliary dyskinesia (PCD) is a disease caused by impaired function of motile cilia. PCD mainly affects the lungs and reproductive organs. Inheritance is autosomal recessive and X-linked. PCD patients have diverse clinical manifestations, thus making the establishment of proper diagnosis challenging. The utility of next-generation sequencing (NGS) technology for diagnostic purposes allows for better understanding of the PCD genetic background. However, identification of specific disease-causing variants is difficult. The main aim of this study was to create a unique guideline that will enable the standardization of the assessment of novel genetic variants within PCD-associated genes. The designed pipeline consists of three main steps: (1) sequencing, detection, and identification of genes/variants, (2) classification of variants according to their effect, and (3) variant characterization using in silico structural and functional analysis. The pipeline was validated through the analysis of the variants detected in a well-known PCD disease-causing gene (DNAI1) and the novel candidate gene (SPAG16). The application of this pipeline resulted in identification of potential disease-causing variants, as well as validation of the variants pathogenicity, through their analysis on transcriptional, translational, and posttranslational levels. The application of this pipeline leads to the confirmation of PCD diagnosis and enables a shift from candidate to PCD disease-causing gene.

Genetic material in all cellular organisms is packed into chromosomes, which represent essential units of inheritance, recombination, and evolution [...] Published version

Distinctive colour patterns in dogs are an integral component of canine diversity. Colour pattern differences are thought to have arisen from mutation and artificial selection during and after domestication from wolves but important gaps remain in understanding how these patterns evolved and are genetically controlled. In other mammals, variation at the ASIP gene controls both the temporal and spatial distribution of yellow and black pigments. Here, we identify independent regulatory modules for ventral and hair cycle ASIP expression, and we characterize their action and evolutionary origin. Structural variants define multiple alleles for each regulatory module and are combined in different ways to explain five distinctive dog colour patterns. Phylogenetic analysis reveals that the haplotype combination for one of these patterns is shared with Arctic white wolves and that its hair cycle-specific module probably originated from an extinct canid that diverged from grey wolves more than 2 million years ago. Natural selection for a lighter coat during the Pleistocene provided the genetic framework for widespread colour variation in dogs and wolves., Dogs exhibit remarkable variation in colour patterns. Here, the authors identify structural variants of independent regulatory modules for ventral and hair cycle expression of the ASIP gene that explain five distinctive dog colour patterns and trace back the origin of one colour pattern to an extinct canid.

Transposable element sequences are usually vertically inherited but have also spread across taxa via horizontal transfer. Previous investigations of ancient horizontal transfer of transposons have compared consensus sequences, but this method resists detection of recent single or low copy number transfer events. The relationship between humans and domesticated animals represents an opportunity for potential horizontal transfer due to the consistent shared proximity and exposure to parasitic insects, which have been identified as plausible transfer vectors. The relatively short period of extended human–animal contact (tens of thousands of years or less) makes horizontal transfer of transposons between them unlikely. However, the availability of high-quality reference genomes allows individual element comparisons to detect low copy number events. Using pairwise all-versus-all megablast searches of the complete suite of retrotransposons of thirteen domestic animals against human, we searched a total of 27,949,823 individual TEs. Based on manual comparisons of stringently filtered BLAST search results for evidence of vertical inheritance, no plausible instances of HTT were identified. These results indicate that significant recent HTT between humans and domesticated animals has not occurred despite the close proximity, either due to the short timescale, inhospitable recipient genomes, a failure of vector activity, or other factors.

Trio-next generation sequencing is useful to identify undiagnosed inherited diseases. We have attended a patient with trigenic ADH5/ALDH2/ADGRV1 pathogenic variants, which caused two distinct diseases, myelodysplastic syndrome and Usher syndrome. Whole genome sequencing of peripheral blood from the patient and his parents were applied to identify disease-causing genes. Sanger sequencing was performed to validate the identified ADH5/ALDH2/ADGRV1 variants. Our results identified disease-associated variants in ADGRV1 (disease inheritance autosomal recessive) and in ADH5 (disease inheritance also autosomal recessive) and a variant in ALDH2 (disease inheritance autosomal dominant). Although the variants identified in ADH5 and ALDH2 have been reported, their co-existence in association with disease-causing variation in a third gene has not. They broaden the spectrum of ADGRV1 in Usher syndrome. Findings on next generation sequencing guided rapid and accurate diagnosis, resulting in patient-tailored therapeutic intervention., Highlights • Trigenic ADH5 / ALDH2 / ADGRV1 ​variants in myelodysplastic syndrome with Usher syndrome were identified. • Two novel pathogenic frameshift variants in ​ADGRV1 ​in compound heterozygous state with Usher syndrome type II were described. • Findings on next generation sequencing guided rapid and accurate diagnosis, resulting in patient-tailored therapy., ADH5/ALDH/ADGRV1 variants, Myelodysplastic syndrome, Trigenic mutations, Trio-next generation sequencing, Usher syndrome.

Significance Circular chromosomes in rod-shaped bacteria exist inside a cell in two distinct configurations, “transverse” and “longitudinal,” relative to the long cell axis, with chromosomal loci occupying specific cellular locations in both cases. Bacteria with longitudinal chromosome organization (e.g., Caulobacter crescentus) typically tether their origins of replication to the cell membrane and do not undergo overlapping rounds of replication. In contrast, bacteria with transverse organization (e.g., Escherichia coli) orient their chromosomes by an unknown mechanism and have lifestyles compatible with overlapping rounds of replication. Here, we address the relative roles of two major players in chromosome organization–segregation and propose a model of how E. coli maintains chromosome conformation and orientation inside cells and how this organization is propagated over generations., Structural maintenance of chromosomes (SMC) complexes contribute to chromosome organization in all domains of life. In Escherichia coli, MukBEF, the functional SMC homolog, promotes spatiotemporal chromosome organization and faithful chromosome segregation. Here, we address the relative contributions of MukBEF and the replication terminus (ter) binding protein, MatP, to chromosome organization–segregation. We show that MukBEF, but not MatP, is required for the normal localization of the origin of replication to midcell and for the establishment of translational symmetry between newly replicated sister chromosomes. Overall, chromosome orientation is normally maintained through division from one generation to the next. Analysis of loci flanking the replication termination region (ter), which demark the ends of the linearly organized portion of the nucleoid, demonstrates that MatP is required for maintenance of chromosome orientation. We show that DNA-bound β2-processivity clamps, which mark the lagging strands at DNA replication forks, localize to the cell center, independent of replisome location but dependent on MukBEF action, and consistent with translational symmetry of sister chromosomes. Finally, we directly show that the older (“immortal”) template DNA strand, propagated from previous generations, is preferentially inherited by the cell forming at the old pole, dependent on MukBEF and MatP. The work further implicates MukBEF and MatP as central players in chromosome organization, segregation, and nonrandom inheritance of genetic material and suggests a general framework for understanding how chromosome conformation and dynamics shape subcellular organization.

Dominance is a basic property of inheritance systems describing the link between a diploid genotype at a single locus and the resulting phenotype. Models for the evolution of dominance have long been framed as an opposition between the irreconcilable views of Fisher in 1928 supporting the role of largely elusive dominance modifiers and Wright in 1929, who viewed dominance as an emerging property of the structure of enzymatic pathways. Recent theoretical and empirical advances however suggest that these opposing views can be reconciled, notably using models investigating the regulation of gene expression and developmental processes. In this more comprehensive framework, phenotypic dominance emerges from departures from linearity between any levels of integration in the genotype-to-phenotype map. Here, we review how these different models illuminate the emergence and evolution of dominance. We then detail recent empirical studies shedding new light on the diversity of molecular and physiological mechanisms underlying dominance and its evolution. By reconciling population genetics and functional biology, we hope our review will facilitate cross-talk among research fields in the integrative study of dominance evolution.

In medical genetics, the vast majority of patients with a currently known genetic basis harbor a rare deleterious allele explaining its Mendelian inheritance. Increasingly, for these phenotypes, we recognize exceptions to Mendelian expectations from non-penetrance of clinical disease to significant inter-individual variation in clinical manifestations, likely reflecting the actions of additional modifier genes. Despite recent progress, we still remain ignorant about the molecular basis for many rare disorders presumed to be Mendelian. The molecular evidence increasingly suggests a role for multiple genes in some of these cases, but for how many? In this article, I discuss why equating a phenotype as Mendelian or complex may be short-sighted or even erroneous. As we learn more about the functions of the human genome with its genes in networks, we should view the phenotype of an individual patient as arising from his or her total genomic deleterious burden in a set of functionally inter-related genes affecting that phenotype. This can sometimes arise from deleterious allele(s) at a single gene (Mendelian inheritance) creating a specific biochemical deficiency (or excess) but could just as frequently arise from the cumulative effects of multiple disease alleles (complex inheritance) leading to the same biochemical deficiency (or excess).

This study evaluated the hypothesis that the maternal metabolic stressed status could be inherited to their F1 daughters via epigenetic mechanism. The maternal cow blood β-hydroxybutyric acid (BHB) level (≥0.9 mM/L) was used as an indicator of maternal metabolic stress. Eight newborn daughters' blood cells were used for methylation comparison and analysis. By Whole Genome Bisulphite Sequencing (WGBS), a total of 1,861 Differentially Methylated Regions (DMRs), including 944 differentially methylated cytosines (DMCs), were identified. Most DMRs were distributed in intronic and intergenic regions, and most of the DMR in promoter regions were hypermethylated. Differentially methylated genes (DMGs) with DMR methylation differences higher than 20% were mainly enriched in metabolism-related pathways. These results suggest that newborn calves' metabolic pathways were altered, with 64 DMGs being clustered with metabolic signalling by KEGG analysis. Our study revealed the whole epigenetic landscape of calf blood cells and suggested that the maternal metabolic status can affect the embryo's epigenetic status and metabolic-related pathways in offspring, providing further evidence for epigenetic intergenerational inheritance of metabolic stress in domestic animals. Besides, this study also contributed more evidence to support the Developmental Origins of Health and Disease (DOHAD) theory in large animals.

There are increasing calls to incorporate developmental plasticity into the framework of eco-evolutionary dynamics. The current way is via genotype-specified reaction norms in which inheritance and phenotype expression are gene-based. I propose a developmental system perspective in which phenotypes are formed during individual development in a process comprising a complex set of interactions that involve genes, biochemistry, somatic state, and the (a)biotic environment, and where the developmental system is the unit of phenotype evolution. I explain how the two perspectives differ in assumptions and predictions, which can be contrasted using cue-and-response systems of anticipatory or mitigating developmental plasticity. This can lead to new ways of eco-evolutionary thinking, and deliver important explanations of how populations respond to environmental change through evolved developmental plasticity.

Summary/AbstractWhole-genome duplications yield varied chromosomal pairing patterns, ranging from strictly bivalent to multivalent, resulting in disomic and polysomic inheritance modes. In the bivalent case, homeologous chromosomes form pairs, where in a multivalent pattern all copies are homologous and are therefore free to pair and recombine. As sufficient sequencing data is more readily available than high-quality cytological assessments of meiotic behavior or population genetic assessment of allelic segregation, especially for non-model organisms, here we describe two bioinformatics approaches to infer origins and inheritance modes of polyploids using short-read sequencing data. The first approach is based on distributions of allelic read depth at the heterozygous sites within an individual, as the expectations of such distributions are different for disomic and polysomic inheritance modes. The second approach is more laborious and based on a phylogenetic assessment of partially phased haplotypes of a polyploid in comparison to the closest diploid relatives. We discuss the sources of deviations from expected inheritance patterns, advantages and pitfalls of both methods, effects of mating types on the performance of the methods, and possible future developments.

The aim of this study was to determine the gene action and combining ability of durum wheat for grain protein content. During the three year period a diallel cross was carried out with five modern parents of durum wheat – ‘Victoria’, ‘Deni’, ‘Superdur’, ‘Progres’ and ‘Predel’. Ten hybrid combinations and the parents were grown in the experimental field of the Field Crops Institute, Chirpan. The experiment was performed by the randomize block method design in three replications. It was found that in the inheritance of grain protein content dominance and overdominance in positive and negative directions were observed. Statistical processing of the results showed that both additive and non-additive genetic effects have influenced on inheritance. Non-additive gene effects (SCA) had a greater role in inheritance. This suggests that an effective selection for this trait could begin in later generations. The combining ability analysis has identified two good general combinators (Predel and Superdur varieties) that could be used as donors to increase the values of the trait protein content in grain. Several crosses showing positive and significant SCA effects have also been identified, suitable for achieving reliable transgressive genotypes.

In multicellular organisms, cell identity can be maintained through DNA methylation patterns that control gene expression (1). These and other epigenetic marks installed during development require erasure to facilitate zygote totipotency (2). Otherwise, epigenetic information may be transferred, at least transiently, across generations (1, 2). In mammals, epigenetic reprogramming during germ-cell formation and early embryogenesis ensures zygote totipotency (2, 3). Yet-to-be-explored mechanisms appear to exist in other groups (2). This is expected given that zygote totipotency is a general phenomenon (4). In addition, Weismann’s germ–soma divide, manifest in vertebrate animals (1, 2) and subtly recognized for other groups (5 … [↵][1]1Email: fgsoley{at}gmail.com. [1]: #xref-corresp-1-1

Purpose and objectives. To establish the gene interaction types in the performance inheritance, to evaluate the combining abilities and effects of genes for this trait in spring barley accessions. Materials and methods. We investigated 75 F1 spring barley hybrid combinations derived from crossing 25 female forms with three male ones (chaffy and naked). Crossing was conducted in accordance with topcross design. F1 seeds and parents were sown with a cassette breeding planter SKS-6A. Grain pea was the forecrop. The plot area was 0.20 m2. The interrow distance was 0.20 m; the inter-plot tracks were of 0.50 m. Crossings were performed in two replications. Plants were harvested manually, with roots. For structural analysis, 20 typical plants were chosen from each F1 hybrid population, and the performance inheritance was determined by dominance degree (hp). The obtained data were grouped and gene interaction types were determined as per G.M. Beil and R.E. Atkins’s classification. Using two-factor analysis of variance in STATISTICA 10, we found significant differences between the GCA and SCA variances for the performance and evaluated the combining ability effects. Results and discussion. In 2019–2020, the features of 22 spring barley cultivars and three lines were described in terms of the gene interaction types in the performance inheritance and combining ability. On this basis, the prospects of biotype selections were evaluated. In the arid conditions of 2019, F1 only showed positive over dominance, while in favorable 2020 the inheritance types varied from positive to negative overdominance. In the two years, the general combining ability was high in female cultivars Khors and Troian. The male components did not show consistently high GCA for the both years. Hybrids between accessions with a high GCA and accessions with a lower or intermediate GCA may be promising in breeding due appearance of positive transgressions in the offspring. In 2019, the SCA effects were significantly strong in female forms Troian, Datcha, Gladys, Grace, Gatunok, Modern, and Herkules and in male forms Ahrarii and Scrabble. Conclusions. The study found that the gene interaction types in the spring barley performance inheritance depended on cross combinations and growing conditions. In unfavorable 2019, F1 only showed positive overdominance (heterosis), while in favorable 2020, positive overdominance, positive dominance and intermediate inheritance were observed. In 2019–2020, the high GCA was seen in female cultivars Khors and Troian. The strong SCA effects were noticed in female components Troian, Datcha, Gladys, Grace, Gatunok, Modern, and Herkules and male forms Agrarii and Scrabble. The hybrid combinations with the maximum probability of producing transgressive segregants have been selected, Цель и задачи исследования. Целью исследования было установление типа взаимодействия генов при наследовании продуктивности, комбинационной способности и эффектов действия генов по этому признаку у образцов ячменя ярового. Материалы и методы. Изучали 75 гибридных комбинаций F1 ячменя ярового, исходным материалом были 25 материнских и три отцовских компонента разных разновидностей (пленчатые и голозерные), скрещивания проведены по типу топкроссов. Посев семян первого поколения и родительских образцов проведен кассетной селекционной сеялкой СКС-6А. Предшественник – горох на зерно, площадь делянки – 0,20 м2, междурядие – 0,20 м, межделяночные дорожки – 0,50 м. Повторение – двухразовое. Растения собирали вручную с корнями. Для структурного анализа с каждой гибридной популяции F1 отбирали по 20 типичных растений, наследование продуктивности определяли по степени доминантности (hр). Группирование полученных данных и определение типов взаимодействия генов проводили по классификации G.M. Beil и R.E. Atkins. При помощи двухфакторного дисперсионного анализа по программе STATISTICA 10 установлены достоверные различия между вариансами ЗКЗ и СКЗ по признаку продуктивность и определены эффекты комбинационной способности. Обсуждение результатов. У 2019–2020 гг. установлены особенности 22 сортов и трех линий ячменю ярового по типу взаимодействия генов при наследовании продуктивности и комбинационной способности, на основании чего определены перспективы эффективности отбора биотипов. У засушливых условиях 2019 г. у F1 проявилось только положительное сверхдоминирование, в благоприятном 2020 г. – от положительного до отрицательного сверхдоминирования. За два года изучения установлена высокая общая комбинационная способность материнских сортов Хорс и Троян. У отцовских компонентов стабильно высокой ОКС за оба года изучения не установлено. Гибриды между образцами с высоким уровнем ОКС и образцами с более низким или средним уровнем ОКС могут быть перспективными для селекции посредством появлении в потомстве положительных трансгрессий. Достоверно высокие эффекты специфической комбинационной способности были в 2019 р. у материнских компонентов Троян, Datcha, Gladys, Grace, Ґатунок, Модерн, Геркулес и у отцовских Аграрій та Scrabble. Выводы. В результате исследования установлено, что тип взаимодействия генов при наследовании продуктивности у ячменя ярового зависит от комбинации скрещивания и условий года выращивания. В неблагоприятном 2019 г. у F1 проявилось только положительное сверхдоминирование (гетерозис), в благоприятном 2020 г. – положительное сверхдоминирование, положительное доминирование и промежуточное наследование. В 2019–2020 гг. установлена высокая ОКС материнских сортов Хорс и Троян, высокие эффекты СКС материнских компонентов Троян, Datcha, Gladys, Grace, Ґатунок, Модерн, Геркулес и отцовских Аграрій и Scrabble. Выделены гибридные комбинации с наибольшей вероятностью появления трансгрессивных сегрегантов, Мета і задачі дослідження. Метою дослідження було встановлення типу взаємодії генів при успадкуванні продуктивності, комбінаційної здатності та ефектів дії генів за цією ознакою у зразків ячменю ярого. Матеріали та методи. Досліджували 75 гібридних комбінацій F1 ячменю ярого, вихідним матеріалом були 25 материнських та три батьківських компоненти різних різновидностей (плівчасті та голозерні), схрещування проведено за типом топкросів. Сівбу насіння першого покоління та батьківських зразків проведено касетною селекційною сівалкою СКС-6А. Попередник – горох на зерно, площа ділянки – 0,20 м2, міжряддя – 0,20 м, міжділянкові доріжки – 0,50 м. Повторення – дворазове. Рослини збирали вручну з корінням. Для структурного аналізу з кожної гібридної популяції F1 відбирали по 20 типових рослин, успадкування продуктивності визначали за ступенем домінантності (hр). Групування одержаних даних і визначення типів взаємодії генів проводили за класифікацією G.M. Beil і R.E. Atkins. За допомогою двофакторного дисперсійного аналізу по програмі STATISTICA 10 установлено достовірні відмінності між варіансами ЗКЗ і СКЗ за ознакою продуктивність та визначили ефекти комбінаційної здатності. Обговорення результатів. У 2019–2020 рр. установлено особливості 22 сортів і трьох ліній ячменю ярого за типом взаємодії генів при успадкуванні продуктивності та комбінаційною здатністю, на основі чого визначено перспективи ефективності добору біотипів. У посушливих умовах 2019 р. у F1 проявилося лише позитивне наддомінування, в сприятливому 2020 р. – від позитивного до негативного наддомінування. За два роки вивчення встановлено високу загальну комбінаційну здатність материнських сортів Хорс і Троян. У батьківських компонентів стабільно високої ЗКЗ за обидва роки вивчення не встановлено. Гібриди між зразками з високим рівнем ЗКЗ і зразками з більш низьким чи середнім рівнем ЗКЗ можуть бути перспективними для селекції через прояв у потомстві позитивних трансгресій. Достовірно високі ефекти специфічної комбінаційної здатності були в 2019 р. у материнських компонентів Троян, Datcha, Gladys, Grace, Ґатунок, Модерн, Геркулес та у батьківських Аграрій та Scrabble. Висновки. В результаті дослідження встановлено, що тип взаємодії генів при успадкуванні продуктивності у ячменю ярого залежать від комбінації схрещування та умов року вирощування. В несприятливому 2019 р. у F1 проявилось лише позитивне наддомінування (гетерозис), у сприятливому 2020 р. – позитивне наддомінування, позитивне домінування та проміжне успадкування. В 2019–2020 рр. установлено високу ЗКЗ материнських сортів Хорс і Троян, високі ефекти специфічної СКЗ материнських компонентів Троян, Datcha, Gladys, Grace, Ґатунок, Модерн, Геркулес та батьківських Аграрій і Scrabble. Виділено гібридні комбінації з найбільшою вірогідністю виділення трансгресивних сегрегантів

Background: Gene drive technologies (GDTs) bias the inheritance of a genetic element within a population of non-human organisms, promoting its progressive spread across this population. If successful, GDTs may be used to counter intractable problems such as vector-borne diseases. A key issue in the debate on GDTs relates to what governance is appropriate for these technologies. While governance mechanisms for GDTs are to a significant extent proposed and shaped by professional experts, the perspectives of these experts have not been explored in depth.Methods: A total of 33 GDT experts from different professional disciplines were interviewed to identify, better understand, and juxtapose their perspectives on GDT governance. The pseudonymized transcripts were analyzed thematically.Results: Three main themes were identified: (1) engagement of communities, stakeholders, and publics; (2) power dynamics, and (3) decision-making. There was broad consensus amongst respondents that it is important to engage communities, stakeholders, and publics. Nonetheless, respondents had diverging views on the reasons for doing so and the timing and design of engagement. Respondents also outlined complexities and challenges related to engagement. Moreover, they brought up the power dynamics that are present in GDT research. Respondents stressed the importance of preventing the recurrence of historical injustices and reflected on dilemmas regarding whether and to what extent (foreign) researchers can legitimately make demands regarding local governance. Finally, respondents had diverging views on whether decisions about GDTs should be made in the same way as decisions about other environmental interventions, and on the decision-making model that should be used to decide about GDT deployment.Conclusions: The insights obtained in this interview study give rise to recommendations for the design and evaluation of GDT governance. Moreover, these insights point to unresolved normative questions that need to be addressed to move from general commitments to concrete obligations.

Soley (1) argues that our study (2) does not prove that “transgenerational [epigenetic] inheritance serv[es] an adaptive role in evolution” in honey bees. This view misrepresents our intent. Our main findings are that in honey bees 1) DNA methylation profiles are much more similar between fathers and daughters than between unrelated males and females of different generations and 2) DNA methylation profiles are conserved across somatic and germline tissues (2). We are agnostic as to whether DNA methylation … [↵][1]1To whom correspondence may be addressed. Email: boris.yagound{at}sydney.edu.au. [1]: #xref-corresp-1-1

Escalated and inappropriate levels of aggressive behavior referred to as pathological in psychiatry can lead to violent outcomes with detrimental impact on health and society. Early life trauma triggers adulthood violence and criminality, though molecular mechanisms remain elusive. Here, we provide prefrontal cortex and hypothalamus specific transcriptome profiles of peripubertal stress (PPS) exposed Balb/c adult male mice exhibiting escalated aggression and adult female mice resilient to such aberrant behavioral responses. We identify transthyretin (TTR) as a key regulator of PPS induced escalated aggression and its intergenerational inheritance. TTR mediated long-term perturbation in hypothalamic thyroid hormone (TH) availability contributed to male aggressive behavior without affecting circulating hormone. Ttr gene ablation in hypothalamus impaired local TH signaling including levels of TH transporters (Mct8, Oatp1c1), deiodinase 2(DIO2) and TH responsive genes (Nrgn, Trh and Hr). Escalated aggressive behavior and impaired TTR-TH signaling was also inherited in F1 male progenies. Further, we deciphered Ttr promoter hyper methylation in hypothalamus of such abnormally aggressive males across generations. Interestingly prefrontal cortex showed opposite pattern of Ttr expression as well as long term epigenetic changes. Also, T4 increase by levothyroxine in PFC did not produce any behavioral changes. Our findings reveal that trauma during puberty trigger lasting escalated aggression by epigenetic programming of TTR and consequent impaired thyroid availability in brain. TTR-TH signaling in brain can serve as potential target in reversal of escalated aggression and related psychopathologies.

Transgenic plants are produced both to investigate gene function and to confer desirable traits into crops. Transgene copy number is known to influence expression levels, and consequently, phenotypes. Similarly, knowledge of transgene zygosity is desirable for making quantitative assessments of phenotype and tracking the inheritance of transgenes in progeny generations. Since the first transgenic plants were produced, several methods for determining copy number have been applied, including Southern blotting, quantitative real-time PCR, and more recently, sequencing methods; however, each method has specific disadvantages, compromising throughput, accuracy, or expense. Digital PCR (dPCR) divides reactions into partitions, converting the exponential, analogue nature of PCR into a linear, digital signal that allows the frequency of occurrence of specific sequences to be accurately estimated. Confidence increases with the number of partitions; therefore, the availability of emulsion technologies that enable reactions to be divided into tens of thousands of nanodroplets allows accurate determination of copy number in what has become known as digital droplet PCR (ddPCR). ddPCR offers similar benefits of low costs and scalability as other PCR techniques but with superior accuracy and reliability. Graphic abstract: [Image: see text] Digital PCR (dPCR) divides reactions into partitions, converting the exponential, analogue nature of PCR into a linear, digital signal that allows the frequency of transgene copy number to be accurately assessed.

Background Triflumezopyrim, a novel commercialized mesoionic chemical insecticide, has been confirmed as a promising insecticide for efficiently controlling the brown planthopper, Nilaparvata lugens (Stal). Here, a laboratory triflumezopyrim-resistant (TR) strain and an isogenic susceptible (TS) strain were established to characterize the inheritance and fitness costs of triflumezopyrim resistance in N. lugens. Results After 29 generations of successive selection with triflumezopyrim, the TR strain developed a 155.23-fold higher resistance level than the TS strain. The median lethal concentration (LC50 ) values from progenies (F1 RS and F1 SR) of reciprocal crosses between TR and TS strains suggested that triflumezopyrim resistance in N. lugens was autosomal and codominant. Chi-square analyses of self-bred and backcrossed progenies suggested that the resistance results from a polygenic effect. Compared to the TS strain, the TR strain showed a lower relative fitness (0.62) with a significantly decreased female adult period, longevity, total fecundity, egg hatchability, intrinsic rate of increase (r), finite rate of increase (λ), net reproductive rate (R0 ), and prolonged pre-adult period and total preoviposition period (TPOP). Conclusion The inheritance mode of triflumezopyrim resistance in N. lugens was characterized as autosomal, codominant and polygenic. The resistance had a fitness cost, which may be an important factor limiting the evolution of resistance. These findings provide valuable information for optimizing resistance management strategies to delay triflumezopyrim resistance development and maintain sustainable control of N. lugens. © 2021 Society of Chemical Industry.

Epigenetic inheritance refers to the transmission of phenotypes across generations without affecting the genomic DNA sequence. Even though it has been documented in many species in fungi, animals and plants, the mechanisms underlying epigenetic inheritance are not fully uncovered. Epialleles, the heritable units of epigenetic information, can take the form of several biomolecules, including histones and their post-translational modifications (PTMs). Here, we review the recent advances in the understanding of the transmission of histone variants and histone PTM patterns across generations in C. elegans. We provide a general overview of the intergenerational and transgenerational inheritance of histone PTMs and their modifiers and discuss the interplay among different histone PTMs. We also evaluate soma-germ line communication and its impact on the inheritance of epigenetic traits.

High voltage-activated Cav2.3 R-type Ca2+ channels and low voltage-activated Cav3.2 T-type Ca2+ channels were reported to be involved in numerous physiological and pathophysiological processes. Many of these findings are based on studies in Cav2.3 and Cav3.2 deficient mice. Recently, it has been proposed that inbreeding of Cav2.3 and Cav3.2 deficient mice exhibits significant deviation from Mendelian inheritance and might be an indication for potential prenatal lethality in these lines. In our study, we analyzed 926 offspring from Cav3.2 breedings and 1142 offspring from Cav2.3 breedings. Our results demonstrate that breeding of Cav2.3 deficient mice shows typical Mendelian inheritance and that there is no indication of prenatal lethality. In contrast, Cav3.2 breeding exhibits a complex inheritance pattern. It might be speculated that the differences in inheritance, particularly for Cav2.3 breeding, are related to other factors, such as genetic specificities of the mutant lines, compensatory mechanisms and altered sperm activity.

Inherited retinal dystrophies (IRD) are a group of diseases characterized by the loss or dysfunction of photoreceptors and a high genetic and clinical heterogeneity. Currently, over 270 genes have been associated with IRD which makes genetic diagnosis very difficult. The recent advent of next generation sequencing has greatly facilitated the diagnostic process, enabling to provide the patients with accurate genetic counseling in some cases. We studied 92 patients who were clinically diagnosed with IRD with two different custom panels. In total, we resolved 53 patients (57.6%); in 12 patients (13%), we found only one mutation in a gene with a known autosomal recessive pattern of inheritance; and 27 patients (29.3%) remained unsolved. We identified 120 pathogenic or likely pathogenic variants; 30 of them were novel. Among the cone-rod dystrophy patients, ABCA4 was the most common mutated gene, meanwhile, USH2A was the most prevalent among the retinitis pigmentosa patients. Interestingly, 10 families carried pathogenic variants in more than one IRD gene, and we identified two deep-intronic variants previously described as pathogenic in ABCA4 and CEP290. In conclusion, the IRD study through custom panel sequencing demonstrates its efficacy for genetic diagnosis, as well as the importance of including deep-intronic regions in their design. This genetic diagnosis will allow patients to make accurate reproductive decisions, enroll in gene-based clinical trials, and benefit from future gene-based treatments.

Most biologists agree that evolution is contingent on inherited information shaped by natural selection. This apparent consensus could be taken to indicate agreement on the forces shaping evolution, but vivid discussions reveal divergences on how evolution is perceived. The predominant Modern Synthesis (MS) paradigm holds the position that evolution occurs through random changes acting on genomic inheritance. However, studies from recent decades have revealed that evolutionary inheritance also includes DNA-methylation, RNA, symbionts, and culture, among other factors. This has fueled a demand of a broader evolutionary perspective, for example from the proponents of the Extended Evolutionary Synthesis (EES). Despite fundamental disagreements the different views agree that natural selection happens through dissimilar perpetuation of inheritable information. Yet, neither the MS, nor the ESS dwell extensively on the nature of hereditary information. We do - and conclude that information in and of itself is immaterial. We then argue that the quality upon which natural selection acts henceforth is also immaterial. Based on these notions, we arrive at the information-centric Information Continuum Model (ICM) of evolution. The ICM asserts that hereditary information is embedded in diverse physical forms (DNA, RNA, symbionts etc.) representing a continuum of evolutionary qualities, and that information may migrate between these physical forms. The ICM leaves theoretical exploration of evolution unrestricted by the limitations imposed by the individual physical forms wherein the hereditary information is embedded (e.g. genomes). ICM bestows us with a simple heuristic model that adds explanatory dimensions to be considered in the evolution of biological systems.

Recognizing and remembering dangerous pathogens is of the utmost importance for an animal's survival. Nematodes use a digested bacterial small RNA molecule as a cue of pathogenicity. Inheritance of this RNA even protects the progeny from infection.

Studies of sex chromosomes have played a central role in understanding the consequences of suppressed recombination and sex-specific inheritance among several genomic phenomena. However, we argue that these efforts will benefit from a more rigorous examination of haploid UV sex chromosome systems, in which both the female-limited (U) and male-limited (V) experience suppressed recombination and sex-limited inheritance, and both are transcriptionally active in the haploid and diploid states. We review the life cycle differences that generate UV sex chromosomes and genomic data showing that ancient UV systems have evolved independently in many eukaryotic groups, but gene movement on and off the sex chromosomes, and potentially degeneration continue to shape the current gene content of the U and V chromosomes. Although both theory and empirical data show that the evolution of UV sex chromosomes is shaped by many of the same processes that govern diploid sex chromosome systems, we highlight how the symmetrical inheritance between the UV chromosomes provide an important test of sex-limited inheritance in shaping genome architecture. We conclude by examining how genetic conflict (over sexual dimorphism, transmission-ratio distortion, or parent-offspring conflict) may drive gene gain on UV sex chromosomes, and highlight the role of breeding system in governing the action of these processes. Collectively these observations demonstrate the potential for evolutionary genomic analyses of varied UV sex chromosome systems, combined with natural history studies, to understand how genetic conflict shapes sex chromosome gene content.

Almost 150 y ago, Galton (1) pitted “nature” against “nurture.” In asking whether our biological or environmental inheritance is more important in shaping our traits, Galton implicitly suggested that their effects can be separated. Galton’s division has always been too neat. Our genes and environments intertwine to shape our bodies, capacities, and personalities. The “nature vs. nurture” dichotomy is particularly badly strained in interpreting gene-by-environment interactions, in which the effects of genetic variants depend on the environment in which they are expressed (2). Another challenge is gene–environment covariation, in which, for example, people’s genotypes make them more likely to be exposed to particular environments (3). For example, skin tone—a genetically influenced trait—affects access to health care, socioeconomic exposures, and more (4⇓–6). In PNAS, Wu et al. (7) analyze a fascinating source of gene–environment covariation: Our biological parents, who are the sources of our genes, can also shape our environment. Parental effects on environments—on prenatal environment, diet, socioeconomic circumstances, home environments during childhood, and more—may in turn be influenced by the parents’ genes. The alleles of parents can therefore affect a child’s traits either via the effects they have when inherited in the genome (“direct genetic effects”) or via their effect on the environments that parents create (“indirect parental genetic effects”; Fig. 1). Wu et al. provide new tools for studying such indirect parental genetic effects using summary data from genome-wide association studies (GWASs) (i.e., marker-level summaries that authors of GWASs typically release, even when they do not share raw data) and use them to study genetic effects on birth weight and on educational attainment. Fig. 1. Alleles of biological parents can affect a trait of their child either when inherited and expressed in the child’s genome (“direct genetic effects”; dark blue arrow) or when they are expressed in … [↵][1]1To whom correspondence may be addressed. Email: arbelharpak{at}utexas.edu. [1]: #xref-corresp-1-1

Favored characteristics evolve at two roughly-defined rates: selection of fitness < truncation ≈ truncation with fitness. The fastest route is also the most probable path; the path of least selection. When possible, truncations, requiring x ≥ threshold xt, implement least selection for x. Least selection is also speeded by maximal σ (standard deviation) and maximal threshold xt (consistent with some survivors). Least selection applies to both chemical and biological evolution. Non-genetic truncation is free of the Haldane cost of natural selection; and can yield very rapid non-Darwinian evolution. Least selection also unites prior examples of brisk evolution. For example: evolution via ‘starting bloc selection’ (in which initial action is crucial) and ‘chance utility’ (opportune fluctuation) and ‘near-ideal reactions’ (where undependable reactants recurrently yield a product) occur via transitory paths of least selection. Least selection’s optimized path may still be clear even for transitions whose origins are lost. ‘Bayesian convergence’ (which defines a most probable path) is guaranteed by least selection’s extremum. ‘Distribution fitness’ (specific outcomes from diffuse concurrent variation) is least selection from rare highly functional minorities. Inheritance of encoded chemical capabilities emerges because least selection exploits coexistence of templating and catalysis in a single molecular complex. The ‘crescendo’ of codes leading to the Standard Genetic Code is a specific device that makes a least selection. Thus, plausible evolutionary paths reach biological goals via least selections. Extinctions and radiations are events with coercive thresholds, ensuring that Earth’s history reflects truncation/least selection.

We demonstrate the training of Spiking Neural Networks (SNN) in a novel multi-agent Evolutionary Robotics (ER) framework inspired by competitive evolutionary environments in nature. The topology of a SNN along with morphological parameters of the bot it controls in the ER environment is together treated as a phenotype. Rules of the framework select certain bots and their SNNs for reproduction and others for elimination based on their efficacy in capturing food in a competitive environment. While the bots and their SNNs are not explicitly trained to survive or reproduce using loss functions, these drives emerge implicitly as they evolve to hunt food and survive. Their efficiency in capturing food exhibits the evolutionary signature of punctuated equilibrium. We use this signature to compare the performances of two evolutionary inheritance algorithms on the phenotypes, Mutation and Crossover with Mutation, using ensembles of 100 experiments for each algorithm. We find that Crossover with Mutation promotes 40% faster learning in the SNN than mere Mutation with a statistically significant margin.

CRISPR-based gene drives offer promising means to reduce the burden of pests and vector-borne diseases. These techniques consist of releasing genetically modified organisms carrying CRISPR-Cas nucleases designed to bias their inheritance and rapidly propagate desired modifications. Gene drives can be intended to reduce reproductive capacity of harmful insects or spread anti-pathogen effectors through wild populations, even when these confer fitness disadvantages. Technologies capable of halting the spread of gene drives may prove highly valuable in controlling, counteracting, and even reverting their effect on individual organisms as well as entire populations. Here we show engineering and testing of a genetic approach, based on the germline expression of a phage-derived anti-CRISPR protein (AcrIIA4), able to inactivate CRISPR-based gene drives and restore their inheritance to Mendelian rates in the malaria vector Anopheles gambiae. Modeling predictions and cage testing show that a single release of male mosquitoes carrying the AcrIIA4 protein can block the spread of a highly effective suppressive gene drive preventing population collapse of caged malaria mosquitoes., Technologies that can halt the spread of gene drives would be highly useful in controlling or reverting their effect. Here the authors use the anti-CRISPR protein AcrIIA4 to inactivate drives in A. gambiae.

On the basis of findings from developmental biology, some researchers have argued that evolutionary theory needs to be significantly updated. Advocates of such a “developmental update” have, among other things, suggested that we need to re-conceptualize units of selection, that we should expand our view of inheritance to include environmental as well as genetic and epigenetic factors, that we should think of organisms and their environment as involved in reciprocal causation, and that we should reevaluate the rates of evolutionary change. However, many of these same conclusions could be reached on the basis of other evidence, namely from microbiology. In this paper, I ask why microbiological evidence has not had a similarly large influence on calls to update biological theory, and argue that there is no principled reason to focus on developmental as opposed to microbiological evidence in support of these revisions to evolutionary theory. I suggest that the focus on developmental biology is more likely attributable to historical accident. I will also discuss some possible room for overlap between developmental and microbiology, despite the historical separation of these two subdisciplines.

The mechanism of biological information flow is of vital importance. However, traditional research surrounding the genetic code that follows the central dogma to a phenotype faces challengers, including missing heritability and two-phased evolution. Here, we propose the karyotype code, which by organizing genes along chromosomes at once preserves species genome information and provides a platform for other genetic and nongenetic information to develop and accumulate. This specific genome-level code, which exists in all living systems, is compared to the genetic code and other organic codes in the context of information management, leading to the concept of hierarchical biological codes and an ‘extended’ definition of adaptor where the adaptors of a code can be not only molecular structures but also, more commonly, biological processes. Notably, different levels of a biosystem have their own mechanisms of information management, and gene-coded parts inheritance preserves “parts information” while karyotype-coded system inheritance preserves the “system information” which organizes parts information. The karyotype code prompts many questions regarding the flow of biological information, including the distinction between information creation, maintenance, modification, and usage, along with differences between living and non-living systems. How do biological systems exist, reproduce, and self-evolve for increased complexity and diversity? Inheritance is mediated by organic codes which function as informational tools to organize chemical reactions, create new information, and preserve frozen accidents, transforming historical miracles into biological routines.

Inherited epigenetic information has been observed to regulate a variety of complex organismal phenotypes across diverse taxa of life. This continually expanding body of literature suggests that epigenetic inheritance plays a significant, and potentially fundamental, role in inheritance. Despite the important role these types of effects play in biology, the molecular mediators of this non-genetic transmission of information are just now beginning to be deciphered. Here we provide an intellectual framework for interpreting these findings and how they can interact with each other. We also define the different types of mechanisms that have been found to mediate epigenetic inheritance and to regulate whether epigenetic information persists for one or many generations. The field of epigenetic inheritance is entering an exciting phase, in which we are beginning to understand the mechanisms by which non-genetic information is transmitted to, and deciphered by, subsequent generations to maintain essential environmental information without permanently altering the genetic code. A more complete understanding of how and when epigenetic inheritance occurs will advance our understanding of numerous different aspects of biology ranging from how organisms cope with changing environments to human pathologies influenced by a parent’s environment.

It has been suggested that the human species may be undergoing an evolutionary transition in individuality (ETI). But there is disagreement about how to apply the ETI framework to our species, and whether culture is implicated as either cause or consequence. Long-term gene–culture coevolution (GCC) is also poorly understood. Some have argued that culture steers human evolution, while others proposed that genes hold culture on a leash. We review the literature and evidence on long-term GCC in humans and find a set of common themes. First, culture appears to hold greater adaptive potential than genetic inheritance and is probably driving human evolution. The evolutionary impact of culture occurs mainly through culturally organized groups, which have come to dominate human affairs in recent millennia. Second, the role of culture appears to be growing, increasingly bypassing genetic evolution and weakening genetic adaptive potential. Taken together, these findings suggest that human long-term GCC is characterized by an evolutionary transition in inheritance (from genes to culture) which entails a transition in individuality (from genetic individual to cultural group). Thus, research on GCC should focus on the possibility of an ongoing transition in the human inheritance system.

Trypanosoma cruzi, as other kinetoplastids, has a complex mechanism of editing of mitochondrial mRNAs that requires guide RNAs (gRNAs) coded in DNA minicircles in the kinetoplast. There are many variations on this mechanism among species. mRNA editing and gRNA repertoires are almost unknown in T. cruzi. Here, gRNAs were inferred based on deep-sequenced minicircle hypervariable regions (mHVRs) and editing cascades were rebuilt in strains belonging to the six main T. cruzi lineages. Inferred gRNAs were clustered according to their sequence similarity to constitute gRNA classes. Extreme diversity of gRNA classes was observed, which implied highly divergent gRNA repertoires among different lineages, even within some lineages. In addition, a variable gRNA class redundancy (i.e., different gRNA classes editing the same mRNA region) was detected among strains. Some strains had upon four times more gRNA classes than others. Such variations in redundancy affected gRNA classes of all mRNAs in a concerted way, i.e., there are correlated variations in the number of gRNAs classes editing each mRNA. Interestingly, cascades were incomplete for components of the respiratory complex I in several strains. Finally, gRNA classes of different strains may potentially edit mitochondrial mRNAs from other lineages in the same way as they edit their own mitochondrial mRNAs, which is a prerequisite for biparental inheritance of minicircle in hybrids. We propose that genetic exchange and biparental inheritance of minicircles combined with minicircle drift due to (partial) random segregation of minicircles during kDNA replication is a suitable hypothesis to explain the divergences among strains and the high levels of gRNA redundancy in some strains. In addition, our results support that the complex I may not be required in some stages in the life cycle as previously shown and that linkage (in the same minicircle) of gRNAs that edit different mRNAs may prevent gRNA class lost in such stage. Fil: Rusman, Fanny. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Patología Experimental. Universidad Nacional de Salta. Facultad de Ciencias de la Salud. Instituto de Patología Experimental; Argentina Fil: Floridia Yapur, Noelia Aldana del Rosario. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Patología Experimental. Universidad Nacional de Salta. Facultad de Ciencias de la Salud. Instituto de Patología Experimental; Argentina Fil: Tomasini, Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Patología Experimental. Universidad Nacional de Salta. Facultad de Ciencias de la Salud. Instituto de Patología Experimental; Argentina Fil: Diosque, Patricio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Salta. Instituto de Patología Experimental. Universidad Nacional de Salta. Facultad de Ciencias de la Salud. Instituto de Patología Experimental; Argentina

Hearing impairment (HI) is one of the most common sensory disabilities with exceptionally high genetic heterogeneity. Of genetic HI cases, 30% are syndromic and 70% are nonsyndromic. For nonsyndromic (NS) HI, 77% of the cases are due to autosomal recessive (AR) inheritance. ARNSHI is usually congenital/prelingual, severe-to-profound, affects all frequencies and is not progressive. Thus far, 73 ARNSHI genes have been identified. Populations with high rates of consanguinity have been crucial in the identification of ARNSHI genes, and 92% (67/73) of these genes were identified in consanguineous families. Recent changes in genomic technologies and analyses have allowed a shift towards ARNSHI gene discovery in outbred populations. The latter is crucial towards understanding the genetic architecture of ARNSHI in diverse and understudied populations. We present an overview of the 73 ARNSHI genes, the methods used to identify them, including next-generation sequencing which revolutionized the field, and new technologies that show great promise in advancing ARNSHI discoveries.

This study were implemented within four growing seasons from 2017/2018 to 2020/2021. The five populations (P1, P2, F1, F2 and F3) of two crosses of bread wheat (Misr 3 x Shandaweel-1 and Giza 168 x Sakha 94) were evaluated in two locations during 2020/2021 growing season, at West West El-Minia and Sids Agricultural Research Station, Agricultural Research Center, Egypt, In order to determine the mode of gene action and the inheritance pattern of plant height, no. of spikes plant-1, no. of kernels spike-1, 100-kernel weight and grain yield plant-1. The t-test showed significant differences among parental genotypes of each cross for all studied characters. The mean effects (m) were highly significant for all characters under the study in the two crosses and locations, indicating the ability to enhance the performance of these characters by pedigree selection. Scaling test revealed the presence of nonallelic interactions (epistasis) in the most studied characters. Dominance gene effects were generally greater than additive ones in most characters. Gene effects varied among characters, whereas the dominance and duplicate dominance beside additive gene effects were found to play important role in the inheritance of most studied characters. The desired significant and highly significant positive heterotic effects to mid-parents for two crosses were detected in the two locations. Broad sense heritability estimates displayed moderate values in most characters. The highest expected genetic gain was found to be correlated with high heritability in narrow sense estimated in all studied characters.

In a changing environment, small RNAs (sRNAs) play an important role in the post-transcriptional regulation of gene expression and can vary in abundance depending on the conditions experienced by an individual (phenotypic plasticity) and its parents (non-genetic inheritance). Many sRNAs are unusual in that they can be produced in two ways, either using genomic DNA as the template (primary sRNAs) or existing sRNAs as the template (secondary sRNAs). Thus, organisms can evolve rapid plastic responses to their current environment by adjusting the amplification rate of sRNA templates. sRNA levels can also be transmitted transgenerationally by the direct transfer of either sRNAs or the proteins involved in amplification. Theory is needed to describe the selective forces acting on sRNA levels, accounting for the dual nature of sRNAs as regulatory elements and templates for amplification and for the potential to transmit sRNAs and their amplification agents to offspring. Here, we develop a model to study the dynamics of sRNA production and inheritance in a fluctuating environment. We tested the selective advantage of mutants capable of sRNA-mediated phenotypic plasticity within resident populations with fixed levels of sRNA transcription. Even when the resident was allowed to evolve an optimal constant rate of sRNA production, plastic amplification rates capable of responding to environmental conditions were favored. Mechanisms allowing sRNA transcripts or amplification agents to be inherited were favored primarily when parents and offspring face similar environments and when selection acts before the optimal level of sRNA can be reached within the organism. Our study provides a clear set of testable predictions for the evolution of sRNA-related mechanisms of phenotypic plasticity and transgenerational inheritance., Author summary Small RNAs (sRNA) are produced by a wide range of organisms, from bacteria to plants and animals. These molecules are involved in the response to environmental stress (e.g., temperature, pathogens) and can be transmitted across generations. We developed a model to explore the dynamics of sRNA production (phenotypic plasticity) and inheritance in a fluctuating environment. We tested whether different sRNA mutants can invade a population where individuals produce sRNA at a constant optimal transcription rate. In our simulations, plastic amplification rates capable of responding to environmental conditions were favored and the transmission of sRNA transcripts or amplification agents across generations was particularly advantageous when parents and offspring faced similar environments. sRNA amplification alone is not favored except when optimal sRNA levels are not reached within a generation. Our model provides novel predictions for the molecular mechanisms of sRNA production and guidance for future empirical studies on mutations that impair the mechanisms of sRNA production and their fitness consequences.

Behavioral genetics and cultural evolution have both revolutionized our understanding of human behavior – largely independent of each other. Here, we reconcile these two fields under a dual inheritance framework, offering a more nuanced understanding of the interaction between genes and culture. Going beyond typical analyses of gene–environment interactions, we describe the cultural dynamics that shape these interactions by shaping the environment and population structure. A cultural evolutionary approach can explain, for example, how factors such as rates of innovation and diffusion, density of cultural subgroups, and tolerance for behavioral diversity impact heritability estimates, thus yielding predictions for different social contexts. Moreover, when cumulative culture functionally overlaps with genes, genetic effects become masked, unmasked, or even reversed, and the causal effects of an identified gene become confounded with features of the cultural environment. The manner of confounding is specific to a particular society at a particular time, but a WEIRD (western, educated, industrialized, rich, and democratic) sampling problem obscures this boundedness. Cultural evolutionary dynamics are typically missing from models of gene-to-phenotype causality, hindering generalizability of genetic effects across societies and across time. We lay out a reconciled framework and use it to predict the ways in which heritability should differ between societies, between socioeconomic levels, and other groupings within some societies but not others, and over the life course. An integrated cultural evolutionary behavioral genetic approach cuts through the nature–nurture debate and helps resolve controversies in topics such as IQ.

Apart from carrying hereditary information inherited from their ancestors and being able to pass on the information to their descendants, cells can also inherit and transmit information that is not stored as changes in their genome sequence. Such epigenetic cell memory, which is particularly important in multicellular organisms, involves multiple biochemical modules mainly including chromatin organization, epigenetic modification and gene transcription. The synergetic mechanism among these three modules remains poorly understood and how they collaboratively affect the robustness and stability of epigenetic memory is unclear either. Here we developed a multiscale model to address these questions. We found that the chromatin organization driven by long-range epigenetic modifications can significantly enhance epigenetic cell memory and its stability in contrast to that driven by local interaction and that chromatin topology and gene activity can promptly and simultaneously respond to changes in nucleosome modifications while maintaining the robustness and stability of epigenetic cell memory over several cell cycles. We concluded that the synergism between chromatin dynamics and gene transcription facilitates the faithful inheritance of epigenetic cell memory across generations.

Evidence for a biparental mode of mitochondrial DNA (mtDNA) inheritance has been sparse and remains controversial. Recent studies using a range of complementary techniques do not support paternal transmission of mtDNA and highlight the co-amplification of rare, concatenated nuclear mtDNA segments as a technical artefact that may explain previous observations. This Comment discusses recent studies supporting the existence of concatenated mitochondrial DNA (mtDNA) segments integrated into the nuclear genome, which may explain previous observations suggesting the existence of a biparental mode of mtDNA inheritance.

Environmental factors can trigger cellular responses that propagate across mitosis or even generations. Perturbations to the epigenome could underpin such acquired changes, however, the extent and contexts in which modified chromatin states confer heritable memory in mammals is unclear. Here we exploit a modular epigenetic editing strategy to establish de novo heterochromatin domains (epialleles) at endogenous loci and track their inheritance in a developmental model. We find that naïve pluripotent phases systematically erase ectopic domains of heterochromatin via active mechanisms, which acts as an intergenerational safeguard against transmission of epialleles. Upon lineage specification however, acquired chromatin states can be probabilistically inherited under selectively favourable conditions, including propagation of p53 silencing through in vivo development. Using genome-wide CRISPR screening, we identify the mechanisms that block heritable silencing memory in pluripotent cells, and demonstrate removal of Dppa2 unlocks the potential for epigenetic inheritance uncoupled from DNA sequence. Our study outlines a mechanistic basis for how epigenetic inheritance is restricted in mammals, and reveals genomic- and developmental-contexts in which heritable memory is feasible.

Color polymorphisms are widely studied to identify the mechanisms responsible for the origin and maintenance of phenotypic variability in nature. Two of the mechanisms of balancing selection currently thought to explain the long-term persistence of polymorphisms are the evolution of alternative phenotypic optima through correlational selection on suites of traits including color and heterosis. Both of these mechanisms can generate differences in offspring viability and fitness arising from different morph combinations. Here, we examined the effect of parental morph combination on fertilization success, embryonic viability, newborn quality, antipredator, and foraging behavior, as well as inter-annual survival by conducting controlled matings in a polymorphic lacertid Podarcis muralis, where color morphs are frequently assumed to reflect alternative phenotypic optima (e.g., alternative reproductive strategies). Juveniles were kept in outdoor tubs for a year in order to study inter-annual growth, survival, and morph inheritance. In agreement with a previous genome-wide association analysis, morph frequencies in the year-old juveniles matched the frequencies expected if orange and yellow expressions depended on recessive homozygosity at 2 separate loci. Our findings also agree with previous literature reporting higher reproductive output of heavy females and the higher overall viability of heavy newborn lizards, but we found no evidence for the existence of alternative breeding investment strategies in female morphs, or morph-combination effects on offspring viability and behavior. We conclude that inter-morph breeding remains entirely viable and genetic incompatibilities are of little significance for the maintenance of discrete color morphs in P. muralis from the Pyrenees.

If genetics defines the inheritance of DNA, epigenetics aims to regulate and make it adaptable. Epigenetic alterations include DNA methylation, chromatin remodelling, post-translational modifications of histone proteins and activity of non-coding RNAs. Several studies, especially in animal models, have reported transgenerational inheritance of epigenetic marks. However, evidence of transgenerational inheritance in humans via germline in the absence of any direct exposure to the driving external stimulus remains controversial. Most of the epimutations exist in relation with genetic variants. The present review looks at intergenerational and transgenerational inheritance in humans, (both father and mother) in response to diet, exposure to chemicals, stress, exercise, and disease status. If not transgenerational, at least intergenerational human studies could help to understand early processes of inheritance. In humans, female and male germline development follow separate paths of epigenetic events and both oocyte and sperm possess their own unique epigenomes. While DNA methylation alterations are reset during epigenetic reprogramming, non-coding RNAs via human sperm provide evidence of being reliable carriers for transgenerational inheritance. Human studies reveal that one mechanism of epigenetic inheritance cannot be applied to the complete human genome. Multiple factors including time, type, and tissue of exposure determine if the modified epigenetic mark could be transmissible and till which generation. Population-specific differences should also be taken into consideration while associating inheritance to an environmental exposure. A longitudinal study targeting one environmental factor, but different population groups should be conducted at a specific geographical location to pinpoint heritable epigenetic changes.

DNA double-strand breaks (DSBs), interrupting the genetic information, are elicited by various environmental and endogenous factors. They bear the risk of cell lethality and, if mis-repaired, of deleterious mutation. This negative impact is contrasted by several evolutionary achievements for DSB processing that help maintaining stable inheritance (correct repair, meiotic cross-over) and even drive adaptation (immunoglobulin gene recombination), differentiation (chromatin elimination) and speciation by creating new genetic diversity via DSB mis-repair. Targeted DSBs play a role in genome editing for research, breeding and therapy purposes. Here, I survey possible causes, biological effects and evolutionary consequences of DSBs, mainly for students and outsiders.