Inheritance Of Variation Research Articles

Paternal Inheritance of Mitochondrial DNA May Lead to Dioecy in Conifers

In angiosperms cytoplasmic DNA is typically passed on maternally through ovules. Genes in the mtDNA may cause male sterility. When male-sterile (female) cytotypes produce more seeds than cosexuals, they pass on more copies of their mtDNA and will co-occur with cosexuals with a neutral cytotype. Cytoplasmic gynodioecy is a well-known phenomenon in angiosperms, both in wild and crop plants. In some conifer families (e.g. Pinaceae) mitochondria are also maternally inherited. However in some other families (e.g. Taxaceae and Cupressaceae) mtDNA is paternally inherited through the pollen. With paternal mtDNA inheritance, male cytotypes that produce more pollen than cosexuals are expected to co-occur with cosexuals. This is uncharted territory. An ESS model shows that the presence of male cytotypes selects for more female allocation in the cosexual, i.e. for sexual specialisation. An allele that switches sex from male to female can then invade. This leads to rapid loss of the neutral cytotype of the cosexual, fixation of the male cytotype and dioecy with 50% males and 50% females. The models suggest that paternal inheritance of mtDNA facilitates the evolution dioecy. Consistent with this hypothesis the Pinaceae are 100% monoecious, while dioecy is common in the Taxaceae family and in the genus Juniperus (Cupressaceae). However, no reliable data are yet available on both mode of inheritance of mtDNA and gender variation of the same species. When cosexuals benefit from reproductive assurance (high selfing rate, low inbreeding depression, low fertilisation) they maintain themselves next to males and females. This predicted pattern with three sex types present in the same population is observed in conifers in nature.

Genome-wide association and environmental suppression of the mortal germline phenotype of wild C. elegans.

The animal germline lineage needs to be maintained along generations. However, some Caenorhabditis elegans wild isolates display a mortal germline phenotype, leading to sterility after several generations at 25°C. Using a genome-wide association approach, we detect a significant peak on chromosome III around 5 Mb, confirmed by introgressions. Thus, a seemingly deleterious genotype is maintained at intermediate frequency in the species. Environmental rescue is a likely explanation, and indeed associated bacteria and microsporidia suppress the phenotype of wild isolates as well as mutants in small RNA inheritance (nrde-2) and histone modifications (set-2). Escherichia coli strains of the K-12 lineage suppress the phenotype compared to B strains. By shifting a wild strain from E. coli K-12 to E. coli B, we find that memory of the suppressing condition is maintained over several generations. Thus, the mortal germline phenotype of wild C. elegans is in part revealed by laboratory conditions and may represent variation in epigenetic inheritance and environmental interactions. This study also points to the importance of non-genetic memory in the face of environmental variation.

Light-driven eco-evolutionary dynamics in a synthetic replicator system.

Darwinian evolution involves the inheritance and selection of variations in reproducing entities. Selection can be based on, among others, interactions with the environment. Conversely, the replicating entities can also affect their environment generating a reciprocal feedback on evolutionary dynamics. The onset of such eco-evolutionary dynamics marks a stepping stone in the transition from chemistry to biology. Yet the bottom-up creation of a molecular system that exhibits eco-evolutionary dynamics has remained elusive. Here we describe the onset of such dynamics in a minimal system containing two synthetic self-replicators. The replicators are capable of binding and activating a co-factor, enabling them to change the oxidation state of their environment through photoredox catalysis. The replicator distribution adapts to this change and, depending on light intensity, one or the other replicator becomes dominant. This study shows how behaviour analogous to eco-evolutionary dynamics-which until now has been restricted to biology-can be created using an artificial minimal replicator system.

The contributions of rare inherited and polygenic risk to ASD in multiplex families

Autism spectrum disorder (ASD) has a complex genetic architecture involving contributions from both de novo and inherited variation. Few studies have been designed to address the role of rare inherited variation or its interaction with common polygenic risk in ASD. Here, we performed whole-genome sequencing of the largest cohort of multiplex families to date, consisting of 4,551 individuals in 1,004 families having two or more autistic children. Using this study design, we identify seven previously unrecognized ASD risk genes supported by a majority of rare inherited variants, finding support for a total of 74 genes in our cohort and a total of 152 genes after combined analysis with other studies. Autistic children from multiplex families demonstrate an increased burden of rare inherited protein-truncating variants in known ASD risk genes. We also find that ASD polygenic score (PGS) is overtransmitted from nonautistic parents to autistic children who also harbor rare inherited variants, consistent with combinatorial effects in the offspring, which may explain the reduced penetrance of these rare variants in parents. We also observe that in addition to social dysfunction, language delay is associated with ASD PGS overtransmission. These results are consistent with an additive complex genetic risk architecture of ASD involving rare and common variation and further suggest that language delay is a core biological feature of ASD.

Demographic turnover can be a leading driver of hierarchy dynamics, and social inheritance modifies its effects.

Individuals and societies are linked through a feedback loop of mutual influence. Demographic turnover shapes group composition and structure by adding and removing individuals, and social inheritance shapes social structure through the transmission of social traits from parents to offspring. Here I examine how these drivers of social structure feedback to influence individual outcomes. I explore these society-to-individual effects in systems with social inheritance of hierarchy position, as occur in many primates and spotted hyenas. Applying Markov chain models to empirical and simulated data reveals how demography and social inheritance interact to strongly shape individual hierarchy positions. In hyena societies, demographic processes-not status seeking-account for the majority of hierarchy dynamics and cause an on-average lifetime decline in social hierarchy position. Simulated societies clarify how social inheritance alters demographic effects-demographic processes cause hierarchy position to regress to the mean, but the addition of social inheritance modifies this pattern. Notably, the combination of social inheritance and rank-related reproductive success causes individuals to decline in rank over their lifespans, as seen in the hyena data. Further analyses explore how 'queens' escape this pattern of decline, and how variation in social inheritance generates variability in reproductive inequality. This article is part of the theme issue 'Evolutionary ecology of inequality'.

Epigenomics in stress tolerance of plants under the climate change.

Epigenomics in stress tolerance of plants under the climate change.

Pharmaco-Omics in Psoriasis: Paving the Way towards Personalized Medicine.

The emergence of high-throughput approaches has had a profound impact on personalized medicine, evolving the identification of inheritable variation to trajectory analyses of transient states and paving the way for the unveiling of response biomarkers. The utilization of the multi-layered pharmaco-omics data, including genomics, transcriptomics, proteomics, and relevant biological information, has facilitated the identification of key molecular biomarkers that can predict the response to therapy, thereby optimizing treatment regiments and providing the framework for a tailored treatment plan. Despite the availability of multiple therapeutic options for chronic diseases, the highly heterogeneous clinical response hinders the alleviation of disease signals and exacerbates the annual burden and cost of hospitalization and drug regimens. This review aimed to examine the current state of the pharmaco-omic approaches performed in psoriasis, a common inflammatory disease of the skin. We sought to identify central studies that investigate the inter-individual variability and explore the underlying molecular mechanisms of drug response progression via biological profiling in psoriatic patients administered with the extended therapeutic armamentarium of psoriasis, incorporating conventional therapies, small molecules, as well as biological drugs that inhibit central pathogenic cytokines involved in the disease pathogenesis.

Inheritance of wood properties and their radial variations in full-sib families of 36-year-old Japanese larch (Larix kaempferi (Lamb.) Carr.)

Key messageLarger differences of maximum load among families were found in mature wood compared to juvenile wood, suggesting the possibility of improving mature wood with higher resistance to rupture and maintaining characteristics of material in Larix kaempferi (Lamb.) Carr. by selecting specific mating parents.ContextBecause the wood from L. kaempferi trees is used for construction lumber, wood properties and bending properties should be focused on as targeted traits of tree breeding programs.AimsWe clarified the radial variation of inheritance for wood properties and bending properties and classified the features of bending properties among families in L. kaempferi.MethodsAnnual ring width, latewood percentage, air-dry density, microfibril angle, modulus of elasticity, modulus of rupture, and bending work at five radial positions were investigated for 15 full-sib families of 36-year-old L. kaempferi grown in two progeny test sites in Japan.ResultsHigher heritability at almost all radial positions was found in air-dry density. Phenotypic and genetic correlations between air-dry density and bending properties showed relatively higher values at almost all radial positions. Load-deflection curves in 15 families could be divided into three groups in juvenile and mature wood. Variation among groups for load-deflection curves in mature wood was relatively larger than that in juvenile wood.ConclusionAir-dry density can be used as a criterion to select trees with superior bending properties. Mature wood in L. kaempferi could be effectively improved by selecting individuals.

Epigenetics for crop adaptation to climate change

Epigenetics for crop adaptation to climate change

Intrinsically disordered BMP4 morphogen and the beak of the finch: Co-option of an ancient axial patterning system

Darwin's finches, with the primary diversity in the shape and size of their beaks, represent an excellent model system to study speciation and adaptive evolution. It is generally held that evolution depends on the natural selection of heritable phenotypic variations originating from the genetic mutations. However, it is now increasingly evident that epigenetic transgenerational inheritance of phenotypic variation can also guide evolutionary change. Several studies have shown that the bone morphogenetic protein BMP4 is a major driver of beak morphology. A recent study explored variability of the morphological, genetic, and epigenetic differences in the adjacent “urban” and “rural” populations of two species of Darwin's finches on the Galápagos Islands and revealed significant changes in methylation patterns in several genes including those involved in the BMP/TGFß pathway in the sperm DNA compared to erythrocyte DNA. These observations indicated that epigenetic changes caused by environmental fluctuations can be passed on to the offspring. Nonetheless, the mechanism by which dysregulated expression of BMP4 impacts beak morphology remains poorly understood. Here, we show that BMP4 is an intrinsically disordered protein and present a causal a link between epigenetic changes, BMP4 dysregulation and the evolution of the beak of the finch by natural selection.

Radial variations of broad-sense heritability in wood properties and classification of load\u2013deflection curves in static bending for six half-sib families of Chamaecyparis obtusa

Wood properties (annual ring width, tracheid length, microfibril angle [MFA], basic density, and air-dry density) and mechanical properties (modulus of elasticity [MOE], modulus of rupture [MOR], bending work, and compressive strength) in 34-year-old Chamaecyparis obtusa trees of six half-sib families were measured from pith to bark to clarify radial variations in inheritance of these traits and the relationships between wood properties and mechanical properties. In addition, within-tree and among-family differences in the load–deflection curves were discussed. Radial variations of all wood properties were fitted to linear or nonlinear mixed-effects models with random effects of families. The MFA was correlated with MOE in all radial positions, whereas air-dry density correlated with all mechanical properties in mature wood. Radial variations in broad-sense heritability differed between wood properties. A relatively higher broad-sense heritability was recognized in almost all wood properties for mature wood. Based on the results, it was concluded that mechanical properties in mature wood can be effectively improved using MFA and air-dry density as criteria. In addition, the types of load–deflection curve in mature wood differed from those in juvenile wood, suggesting that not only elastic properties, but also plastic properties in C. obtusa are affected by genetic controls, especially in mature wood.

Human genetic analyses of organelles highlight the nucleus in age-related trait heritability.

Most age-related human diseases are accompanied by a decline in cellular organelle integrity, including impaired lysosomal proteostasis and defective mitochondrial oxidative phosphorylation. An open question, however, is the degree to which inherited variation in or near genes encoding each organelle contributes to age-related disease pathogenesis. Here, we evaluate if genetic loci encoding organelle proteomes confer greater-than-expected age-related disease risk. As mitochondrial dysfunction is a 'hallmark' of aging, we begin by assessing nuclear and mitochondrial DNA loci near genes encoding the mitochondrial proteome and surprisingly observe a lack of enrichment across 24 age-related traits. Within nine other organelles, we find no enrichment with one exception: the nucleus, where enrichment emanates from nuclear transcription factors. In agreement, we find that genes encoding several organelles tend to be 'haplosufficient,' while we observe strong purifying selection against heterozygous protein-truncating variants impacting the nucleus. Our work identifies common variation near transcription factors as having outsize influence on age-related trait risk, motivating future efforts to determine if and how this inherited variation then contributes to observed age-related organelle deterioration.

Inheritance of DNA methylation differences in the mangrove Rhizophora mangle.

The capacity to respond to environmental challenges ultimately relies on phenotypic variation which manifests from complex interactions of genetic and nongenetic mechanisms through development. While we know something about genetic variation and structure of many species of conservation importance, we know very little about the nongenetic contributions to variation. Rhizophora mangle is a foundation species that occurs in coastal estuarine habitats throughout the neotropics where it provides critical ecosystem functions and is potentially threatened by anthropogenic environmental changes. Several studies have documented landscape-level patterns of genetic variation in this species, but we know virtually nothing about the inheritance of nongenetic variation. To assess one type of nongenetic variation, we examined the patterns of DNA sequence and DNA methylation in maternal plants and offspring from natural populations of R. mangle from the Gulf Coast of Florida. We used a reduced representation bisulfite sequencing approach (epi-genotyping by sequencing; epiGBS) to address the following questions: (a) What are the levels of genetic and epigenetic diversity in natural populations of R. mangle? (b) How are genetic and epigenetic variation structured within and among populations? (c) How faithfully is epigenetic variation inherited? We found low genetic diversity but high epigenetic diversity from natural populations of maternal plants in the field. In addition, a large portion (up to ~25%) of epigenetic differences among offspring grown in common garden was explained by maternal family. Therefore, epigenetic variation could be an important source of response to challenging environments in the genetically depauperate populations of this foundation species.

Elementary students’ explanation of variation of traits and teacher‘s feedback using an online embedded assessment tool

ABSTRACT Although extensive research has shown the important educational value of technology-enhanced online units on students’ science learning, few studies have looked at upper elementary students' knowledge integration in a web-based inquiry science environment (WISE). This case study investigates how upper-elementary students responded to an online prompt, in an embedded assessment tool, to construct a scientific explanation around the variation of traits in their class and how a teacher provided feedback to encourage student discourse. Our findings show that students were able to identify which traits were more common in their class; however, they struggled with making a connection between variation of traits and inheritance of traits when analyzing data from their pie chart. Additionally, we show that an upper-elementary teacher used an embedded assessment tool to scaffold the iterative process of learning and feedback that occurs in an online platform that leverages learning technologies by engaging in high-level discourse moves. We suggest that teachers’ use of embedded assessments in a technology-enhanced environment can encourage student self-reflection and support teachers in making evidence-based instructional decisions as well as provide immediate feedback along the way, which is a key support when students are not participating in traditional face-to-face classroom environments.

OncoGEMINI: software for investigating tumor variants from multiple biopsies with integrated cancer annotations

BackgroundDNA sequencing has unveiled extensive tumor heterogeneity in several different cancer types, with many exhibiting diverse subclonal populations. Identifying and tracing mutations throughout the expansion and progression of a tumor represents a significant challenge. Furthermore, prioritizing the subset of such mutations most likely to contribute to tumor evolution or that could serve as potential therapeutic targets represents an ongoing problem.ResultsHere, we describe OncoGEMINI, a new tool designed for exploring the complex patterns and trajectory of somatic and inherited variation observed in heterogeneous tumors biopsied over the course of treatment. This is accomplished by creating a searchable database of variants that includes tumor sampling time points and allows for filtering methods that reflect specific changes in variant allele frequencies over time. Additionally, by incorporating existing annotations and resources that facilitate the interpretation of cancer mutations (e.g., CIViC, DGIdb), OncoGEMINI enables rapid searches for, and potential identification of, mutations that may be driving subclonal evolution.ConclusionsBy combining relevant genomic annotations alongside specific filtering tools, OncoGEMINI provides powerful and customizable approaches that enable the quick identification of individual tumor variants that meet specified criteria. It can be applied to a wide range of tumor-derived sequence data, but is especially designed for studies with multiple samples, including longitudinal datasets. It is available under an MIT license at github.com/fakedrtom/oncogemini.

Differential DNA methylation in somatic and sperm cells of hatchery vs wild (natural-origin) steelhead trout populations.

Environmental factors such as nutrition, stress, and toxicants can influence epigenetic programming and phenotypes of a wide variety of species from plants to humans. The current study was designed to investigate the impacts of hatchery spawning and rearing on steelhead trout (Oncorhynchus mykiss) vs the wild fish on a molecular level. Additionally, epigenetic differences between feeding practices that allow slow growth (2 years) and fast growth (1 year) hatchery trout were investigated. The sperm and red blood cells (RBC) from adult male slow growth/maturation hatchery steelhead, fast growth/maturation hatchery steelhead, and wild (natural-origin) steelhead were collected for DNA preparation to investigate potential alterations in differential DNA methylation regions (DMRs) and genetic mutations, involving copy number variations (CNVs). The sperm and RBC DNA both had a large number of DMRs when comparing the hatchery vs wild steelhead trout populations. The DMRs were cell type specific with negligible overlap. Slow growth/maturation compared to fast growth/maturation steelhead also had a larger number of DMRs in the RBC samples. A number of the DMRs had associated genes that were correlated to various biological processes and pathologies. Observations demonstrate a major epigenetic programming difference between the hatchery and wild natural-origin fish populations, but negligible genetic differences. Therefore, hatchery conditions and growth/maturation rate can alter the epigenetic developmental programming of the steelhead trout. Interestingly, epigenetic alterations in the sperm allow for potential epigenetic transgenerational inheritance of phenotypic variation to future generations. The impacts of hatchery exposures are not only important to consider on the fish exposed, but also on future generations and evolutionary trajectory of fish in the river populations.

Integration of sperm ncRNA-directed DNA methylation and DNA methylation-directed histone retention in epigenetic transgenerational inheritance

BackgroundEnvironmentally induced epigenetic transgenerational inheritance of pathology and phenotypic variation has been demonstrated in all organisms investigated from plants to humans. This non-genetic form of inheritance is mediated through epigenetic alterations in the sperm and/or egg to subsequent generations. Although the combined regulation of differential DNA methylated regions (DMR), non-coding RNA (ncRNA), and differential histone retention (DHR) have been shown to occur, the integration of these different epigenetic processes remains to be elucidated. The current study was designed to examine the integration of the different epigenetic processes.ResultsA rat model of transiently exposed F0 generation gestating females to the agricultural fungicide vinclozolin or pesticide DDT (dichloro-diphenyl-trichloroethane) was used to acquire the sperm from adult males in the subsequent F1 generation offspring, F2 generation grand offspring, and F3 generation great-grand offspring. The F1 generation sperm ncRNA had substantial overlap with the F1, F2 and F3 generation DMRs, suggesting a potential role for RNA-directed DNA methylation. The DMRs also had significant overlap with the DHRs, suggesting potential DNA methylation-directed histone retention. In addition, a high percentage of DMRs induced in the F1 generation sperm were maintained in subsequent generations.ConclusionsMany of the DMRs, ncRNA, and DHRs were colocalized to the same chromosomal location regions. Observations suggest an integration of DMRs, ncRNA, and DHRs in part involve RNA-directed DNA methylation and DNA methylation-directed histone retention in epigenetic transgenerational inheritance.

Environmental impacts on sperm and oocyte epigenetics affect embryo cell epigenetics and transcription to promote the epigenetic inheritance of pathology and phenotypic variation.

Previous studies have demonstrated that exposure to environmental factors can cause epigenetic modifications to germ cells, particularly sperm, to promote epigenetic and transcriptome changes in the embryo. These germ cell and embryo cell epigenetic alterations are associated with phenotypic changes in offspring. Epigenetic inheritance requires epigenetic changes (i.e. epimutations) in germ cells that promote epigenetic and gene expression changes in embryos. The objective of this perspective is to examine the evidence that germ cell epigenome modifications are associated with embryo cell epigenetic and transcriptome changes that affect the subsequent development of all developing somatic cells to promote phenotype change. Various epigenetic changes in sperm, including changes to histone methylation, histone retention, non-coding RNA expression and DNA methylation, have been associated with alterations in embryo cell epigenetics and gene expression. Few studies have investigated this link for oocytes. The studies reviewed herein support the idea that environmentally induced epigenetic changes in germ cells affect alterations in embryo cell epigenetics and transcriptomes that have an important role in the epigenetic inheritance of pathology and phenotypic change.

基于野外调查和同质种植园实验的芦苇植物功能性状变异研究

研究表型可塑性和遗传变异在植物表型分化中的相对作用，有助于预测全球环境变化下的植物群落组成和生态系统功能的变化。芦苇（Phragmites australis）是全球性广布的草本植物，种内变异丰富，在我国西北和东部均存在多个分化稳定的生态型，但中国芦苇在更大尺度上的表型研究还非常匮乏。将位于黄河上游的宁夏平原和黄河下游的黄河三角洲作为研究区域，通过野外调查和同质种植园实验对芦苇自然种群的植物功能性状变异进行观测。结果表明，无论在野外还是同质种植园，黄河三角洲芦苇的基径、叶长和叶宽均显著大于宁夏平原芦苇，说明两个地区的芦苇种群之间存在着受遗传决定的表型分化，这可能与两个地区间的降水等气候差异有关。在野外，宁夏芦苇的株高和叶厚显著大于黄河三角洲芦苇，但在同质园中差异消失或相反，说明株高、叶厚受环境影响较大，表型可塑性也是芦苇适应环境变化的重要机制。在同质种植园中，宁夏平原芦苇的叶片氮磷含量较低，但株数却显著多于黄河三角洲芦苇，反映了不同地区芦苇之间存在不同的适应策略，宁夏平原芦苇更偏向于高扩散率的杂草策略，而黄河三角洲芦苇更偏向于竞争策略。此外，宁夏平原芦苇的株高、叶长两个性状以及基径-比叶面积相关性在野外和同质园两个环境中存在一致性，表明了性状变异和权衡策略的遗传稳定性。综上，位于黄河上下游的芦苇种群间存在着适应性分化，这是表型可塑性和遗传变异共同作用的结果，不同来源芦苇对全球变化下的多重环境因子的响应还需要进一步研究。;Study on the relative contributions of phenotypic plasticity and genetic variation to plant phenotypic differentiation can facilitate the predictions of community composition and ecosystem functioning under global environmental changes. As a cosmopolitan grass, common reed (Phragmites australis) has a high intraspecific diversity and has several ecotypes in northwest and east China. However, few studies focused on the phenotypic variation of common reed at a larger scale in China. Here, we investigated the intraspecific variation in plant functional traits of P. australis from Ningxia Plain, an upstream wetland, and the Yellow River Delta, a downstream wetland, via field investigation and common garden experiment. The results showed that the shoot diameter, leaf length and leaf width of P. australis from the Yellow River Delta were significantly larger than those from the Ningxia Plain in both the field and the common garden, suggesting a stable phenotypic differentiation controlled by genetic variation between the two regions. The phenotypic differentiation could be explained by the adaptation to local climatic conditions such as precipitation. In the field, the shoot height and the leaf thickness of P. australis from Ningxia Plain were significantly higher than those from the Yellow River Delta, but the difference disappeared or reversed in the common garden, which suggests that these traits are regulated directly by the current environment and phenotypic plasticity is also an important mechanism for P. australis to adapt to environmental changes. In the common garden, the content of nitrogen and phosphorus in leaves of P. australis from Ningxia Plain was lower, while the plant density was significantly larger than that from the Yellow River Delta. Which reflects different adaptive strategies that P. australis from Ningxia Plain prefers a ruderal strategy with a high reproduction rate, while P. australis from the Yellow River Delta favors a competitive strategy. Moreover, there were correlations between the field and the common garden observations in shoot height, leaf length and relationship between shoot diameter and specific leaf area, which indicates the genetic inheritance of trait variation and trade-off strategy. In conclusion, there is an adaptive differentiation between the upstream and downstream populations of P. australis in the Yellow River basin due to phenotypic plasticity and genetic variation. Further studies are needed to reveal the responses of plant from different provenances to future changes of the multiple environmental factors.

Environmentally Induced Epigenetic Transgenerational Inheritance and the Weismann Barrier: The Dawn of Neo-Lamarckian Theory.

For the past 120 years, the Weismann barrier and associated germ plasm theory of heredity have been a doctrine that has impacted evolutionary biology and our concepts of inheritance through the germline. Although August Weismann in his 1872 book was correct that the sperm and egg were the only cells to transmit molecular information to the subsequent generation, the concept that somatic cells do not impact the germline (i.e., the Weismann barrier) is incorrect. However, the doctrine or dogma of the Weismann barrier still influences many scientific fields and topics. The discovery of epigenetics, and more recently environmentally induced epigenetic transgenerational inheritance of phenotypic variation and pathology, have had significant impacts on evolution theory and medicine today. Environmental epigenetics and the concept of epigenetic transgenerational inheritance refute aspects of the Weismann barrier and require a re-evaluation of both inheritance theory and evolution theory.