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ISSUE HIGHLIGHTS [Issue Highlights]

November 2, 2017 - 8:33am
Categories: Genetics News Feed

Moving Speciation Genetics Forward: Modern Techniques Build on Foundational Studies in Drosophila [Ecology and Evolution]

November 2, 2017 - 8:33am

The question of how new species evolve has been examined at every level, from macroevolutionary patterns of diversification to molecular population genetic analyses of specific genomic regions between species pairs. Drosophila has been at the center of many of these research efforts. Though our understanding of the speciation process has grown considerably over the past few decades, very few genes have been identified that contribute to barriers to reproduction. The development of advanced molecular genetic and genomic methods provides promising avenues for the rapid discovery of more genes that contribute to speciation, particularly those involving prezygotic isolation. The continued expansion of tools and resources, especially for species other than Drosophila melanogaster, will be most effective when coupled with comparative approaches that reveal the genetic basis of reproductive isolation across a range of divergence times. Future research programs in Drosophila have high potential to answer long-standing questions in speciation. These include identifying the selective forces that contribute to divergence between populations and the genetic basis of traits that cause reproductive isolation. The latter can be expanded upon to understand how the genetic basis of reproductive isolation changes over time and whether certain pathways and genes are more commonly involved.

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Cell Biology of the Mitochondrion [Cell and Organelle Biology]

November 2, 2017 - 8:33am

Mitochondria are best known for harboring pathways involved in ATP synthesis through the tricarboxylic acid cycle and oxidative phosphorylation. Major advances in understanding these roles were made with Caenorhabditis elegans mutants affecting key components of the metabolic pathways. These mutants have not only helped elucidate some of the intricacies of metabolism pathways, but they have also served as jumping off points for pharmacology, toxicology, and aging studies. The field of mitochondria research has also undergone a renaissance, with the increased appreciation of the role of mitochondria in cell processes other than energy production. Here, we focus on discoveries that were made using C. elegans, with a few excursions into areas that were studied more thoroughly in other organisms, like mitochondrial protein import in yeast. Advances in mitochondrial biogenesis and membrane dynamics were made through the discoveries of novel functions in mitochondrial fission and fusion proteins. Some of these functions were only apparent through the use of diverse model systems, such as C. elegans. Studies of stress responses, exemplified by mitophagy and the mitochondrial unfolded protein response, have also benefitted greatly from the use of model organisms. Recent developments include the discoveries in C. elegans of cell autonomous and nonautonomous pathways controlling the mitochondrial unfolded protein response, as well as mechanisms for degradation of paternal mitochondria after fertilization. The evolutionary conservation of many, if not all, of these pathways ensures that results obtained with C. elegans are equally applicable to studies of human mitochondria in health and disease.

Categories: Genetics News Feed

AdmixPower: Statistical Power and Sample Size Estimation for Mapping Genetic Loci in Admixed Populations [Methods, Technology, and Resources]

November 2, 2017 - 8:33am

Admixed populations result from recent admixture of two or more ancestral populations with divergent allele frequencies. The genome of each admixed individual is a mosaic of haplotypes inherited from the ancestral populations. Despite the substantial work to assess power and sample size requirements for association mapping in genetically homogeneous populations of European ancestry, power and sample size estimation methods for mapping genes in genetically heterogeneous admixed populations such as African Americans are lacking. Admixture mapping is a method that traces the ancestral origin of disease-susceptibility genetic loci in the admixed population. We developed AdmixPower, a freely available tool set based on the open-source R software, to perform power and sample size analysis for genetically heterogeneous admixed populations considering continuous or dichotomous outcomes with a case-only or case-control study design. AdmixPower can be used to compute the sample size required to achieve investigator-specified statistical power under several key parameters including ancestry odds ratio, genotype risk ratio, parental risk ratio, an underlying genetic risk model, trait type, and admixture model (hybrid-isolation or continuous gene flow model). We demonstrate that differences in the key parameters in the admixed population results in substantial differences in the sample size required to achieve adequate power in admixture mapping studies. Our tool provides a resource for researchers to develop a strategy to minimize cost and maximize the success of identifying disease-susceptibility loci in an admixed population. R code used in the sample size and power analysis is freely available from https://research.cchmc.org/mershalab/Tools.html.

Categories: Genetics News Feed

COMBAT: A Combined Association Test for Genes Using Summary Statistics [Statistical Genetics and Genomics]

November 2, 2017 - 8:33am

Genome-wide association studies (GWAS) have been widely used for identifying common variants associated with complex diseases. Traditional analysis of GWAS typically examines one marker at a time, usually single nucleotide polymorphisms (SNPs), to identify individual variants associated with a disease. However, due to the small effect sizes of common variants, the power to detect individual risk variants is generally low. As a complementary approach to SNP-level analysis, a variety of gene-based association tests have been proposed. However, the power of existing gene-based tests is often dependent on the underlying genetic models, and it is not known a priori which test is optimal. Here we propose a combined association test (COMBAT) for genes, which incorporates strengths from existing gene-based tests and shows higher overall performance than any individual test. Our method does not require raw genotype or phenotype data, but needs only SNP-level P-values and correlations between SNPs from ancestry-matched samples. Extensive simulations showed that COMBAT has an appropriate type I error rate, maintains higher power across a wide range of genetic models, and is more robust than any individual gene-based test. We further demonstrated the superior performance of COMBAT over several other gene-based tests through reanalysis of the meta-analytic results of GWAS for bipolar disorder. Our method allows for the more powerful application of gene-based analysis to complex diseases, which will have broad use given that GWAS summary results are increasingly publicly available.

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A Powerful Framework for Integrating eQTL and GWAS Summary Data [Statistical Genetics and Genomics]

November 2, 2017 - 8:33am

Two new gene-based association analysis methods, called PrediXcan and TWAS for GWAS individual-level and summary data, respectively, were recently proposed to integrate GWAS with eQTL data, alleviating two common problems in GWAS by boosting statistical power and facilitating biological interpretation of GWAS discoveries. Based on a novel reformulation of PrediXcan and TWAS, we propose a more powerful gene-based association test to integrate single set or multiple sets of eQTL data with GWAS individual-level data or summary statistics. The proposed test was applied to several GWAS datasets, including two lipid summary association datasets based on $$\sim 100,000$$ and $$\sim 189,000$$ samples, respectively, and uncovered more known or novel trait-associated genes, showcasing much improved performance of our proposed method. The software implementing the proposed method is freely available as an R package.

Categories: Genetics News Feed

A Powerful Variant-Set Association Test Based on Chi-Square Distribution [Statistical Genetics and Genomics]

November 2, 2017 - 8:33am

Detecting the association between a set of variants and a given phenotype has attracted a large amount of attention in the scientific community, although it is a difficult task. Recently, several related statistical approaches have been proposed in the literature; powerful statistical tests are still highly desired and yet to be developed in this area. In this paper, we propose a powerful test that combines information from each individual single nucleotide polymorphism (SNP) based on principal component analysis without relying on the eigenvalues associated with the principal components. We compare the proposed approach with some popular tests through a simulation study and real data applications. Our results show that, in general, the new test is more powerful than its competitors considered in this study; the gain in detecting power can be substantial in many situations.

Categories: Genetics News Feed

Autosomal Trisomy and Triploidy Are Corrected During Female Meiosis in Caenorhabditis elegans [Genome Integrity and Transmission]

November 2, 2017 - 8:33am

Trisomy and triploidy, defined as the presence of a third copy of one or all chromosomes, respectively, are deleterious in many species including humans. Previous studies have demonstrated that Caenorhabditis elegans with a third copy of the X chromosome are viable and fertile. However, the extra X chromosome was shown to preferentially segregate into the first polar body during oocyte meiosis to produce a higher frequency of euploid offspring than would be generated by random segregation. Here, we demonstrate that extra autosomes are preferentially eliminated by triploid C. elegans and trisomy IV C. elegans. Live imaging of anaphase-lagging chromosomes and analysis of REC-8 staining of metaphase II spindles revealed that, in triploids, some univalent chromosomes do not lose cohesion and preferentially segregate intact into the first polar body during anaphase I, whereas other autosomes segregate chromatids equationally at anaphase I and eliminate some of the resulting single chromatids during anaphase II. We also demonstrate asymmetry in the anaphase spindle, which may contribute to the asymmetric segregation. This study reveals a pathway that allows aneuploid parents to produce euploid offspring at higher than random frequency.

Categories: Genetics News Feed

The Role of Blm Helicase in Homologous Recombination, Gene Conversion Tract Length, and Recombination Between Diverged Sequences in Drosophila melanogaster [Genome Integrity and Transmission]

November 2, 2017 - 8:33am

DNA double-strand breaks (DSBs) are a particularly deleterious class of DNA damage that threatens genome integrity. DSBs are repaired by three pathways: nonhomologous-end joining (NHEJ), homologous recombination (HR), and single-strand annealing (SSA). Drosophila melanogaster Blm (DmBlm) is the ortholog of Saccharomyces cerevisiae SGS1 and human BLM, and has been shown to suppress crossovers in mitotic cells and repair mitotic DNA gaps via HR. To further elucidate the role of DmBlm in repair of a simple DSB, and in particular recombination mechanisms, we utilized the Direct Repeat of white (DR-white) and Direct Repeat of white with mutations (DR-white.mu) repair assays in multiple mutant allele backgrounds. DmBlm null and helicase-dead mutants both demonstrated a decrease in repair by noncrossover HR, and a concurrent increase in non-HR events, possibly including SSA, crossovers, deletions, and NHEJ, although detectable processing of the ends was not significantly impacted. Interestingly, gene conversion tract lengths of HR repair events were substantially shorter in DmBlm null but not helicase-dead mutants, compared to heterozygote controls. Using DR-white.mu, we found that, in contrast to Sgs1, DmBlm is not required for suppression of recombination between diverged sequences. Taken together, our data suggest that DmBlm helicase function plays a role in HR, and the steps that contribute to determining gene conversion tract length are helicase-independent.

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Rapid DNA Synthesis During Early Drosophila Embryogenesis Is Sensitive to Maternal Humpty Dumpty Protein Function [Genome Integrity and Transmission]

November 2, 2017 - 8:33am

Problems with DNA replication cause cancer and developmental malformations. It is not fully understood how DNA replication is coordinated with development and perturbed in disease. We had previously identified the Drosophila gene humpty dumpty (hd), and showed that null alleles cause incomplete DNA replication, tissue undergrowth, and lethality. Animals homozygous for the missense allele, hd272-9, were viable, but adult females had impaired amplification of eggshell protein genes in the ovary, resulting in the maternal effects of thin eggshells and embryonic lethality. Here, we show that expression of an hd transgene in somatic cells of the ovary rescues amplification and eggshell synthesis but not embryo viability. The germline of these mothers remain mutant for the hd272-9 allele, resulting in reduced maternal Hd protein and embryonic arrest during mitosis of the first few S/M nuclear cleavage cycles with chromosome instability and chromosome bridges. Epistasis analysis of hd with the rereplication mutation plutonium indicates that the chromosome bridges of hd embryos are the result of a failed attempt to segregate incompletely replicated sister chromatids. This study reveals that maternally encoded Humpty dumpty protein is essential for DNA replication and genome integrity during the little-understood embryonic S/M cycles. Moreover, the two hd272-9 maternal-effect phenotypes suggest that ovarian gene amplification and embryonic cleavage are two time periods in development that are particularly sensitive to mild deficits in DNA replication function. This last observation has broader relevance for interpreting why mild mutations in the human ortholog of humpty dumpty and other DNA replication genes cause tissue-specific malformations of microcephalic dwarfisms.

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Chromosome Healing Is Promoted by the Telomere Cap Component Hiphop in Drosophila [Genome Integrity and Transmission]

November 2, 2017 - 8:33am

The addition of a new telomere onto a chromosome break, a process termed healing, has been studied extensively in organisms that utilize telomerase to maintain their telomeres. In comparison, relatively little is known about how new telomeres are constructed on broken chromosomes in organisms that do not use telomerase. Chromosome healing was studied in somatic and germline cells of Drosophila melanogaster, a nontelomerase species. We observed, for the first time, that broken chromosomes can be healed in somatic cells. In addition, overexpression of the telomere cap component Hiphop increased the survival of somatic cells with broken chromosomes, while the cap component HP1 did not, and overexpression of the cap protein HOAP decreased their survival. In the male germline, Hiphop overexpression greatly increased the transmission of healed chromosomes. These results indicate that Hiphop can stimulate healing of a chromosome break. We suggest that this reflects a unique function of Hiphop: it is capable of seeding formation of a new telomeric cap on a chromosome end that lacks a telomere.

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A Key Regulator of the Glycolytic and Gluconeogenic Central Metabolic Pathways in Sinorhizobium meliloti [Gene Expression]

November 2, 2017 - 8:33am

The order Rhizobiales contains numerous agriculturally, biotechnologically, and medically important bacteria, including the rhizobia, and the genera Agrobacterium, Brucella, and Methylobacterium, among others. These organisms tend to be metabolically versatile, but there has been relatively little investigation into the regulation of their central carbon metabolic pathways. Here, RNA-sequencing and promoter fusion data are presented to show that the PckR protein is a key regulator of central carbon metabolism in Sinorhizobium meliloti; during growth with gluconeogenic substrates, PckR represses expression of the complete Entner–Doudoroff glycolytic pathway and induces expression of the pckA and fbaB gluconeogenic genes. Electrophoretic mobility shift assays indicate that PckR binds an imperfect palindromic sequence that overlaps the promoter or transcriptional start site in the negatively regulated promoters, or is present in tandem upstream the promoter motifs in the positively regulated promoters. Genetic and in vitro electrophoretic mobility shift assay experiments suggest that elevated concentrations of a PckR effector ligand results in the dissociation of PckR from its target binding site, and evidence is presented that suggests phosphoenolpyruvate may function as the effector. Characterization of missense pckR alleles identified three conserved residues important for increasing the affinity of PckR for its cognate effector molecule. Bioinformatics analyses illustrates that PckR is limited to a narrow phylogenetic range consisting of the Rhizobiaceae, Phyllobacteriaceae, Brucellaceae, and Bartonellaceae families. These data provide novel insights into the regulation of the core carbon metabolic pathways of this pertinent group of α-proteobacteria.

Categories: Genetics News Feed

Diversification of Transcriptional Regulation Determines Subfunctionalization of Paralogous Branched Chain Aminotransferases in the Yeast Saccharomyces cerevisiae [Gene Expression]

November 2, 2017 - 8:33am
Categories: Genetics News Feed

Extended Synaptotagmin Localizes to Presynaptic ER and Promotes Neurotransmission and Synaptic Growth in Drosophila [Cellular Genetics]

November 2, 2017 - 8:33am

The endoplasmic reticulum (ER) is an extensive organelle in neurons with important roles at synapses including the regulation of cytosolic Ca2+, neurotransmission, lipid metabolism, and membrane trafficking. Despite intriguing evidence for these crucial functions, how the presynaptic ER influences synaptic physiology remains enigmatic. To gain insight into this question, we have generated and characterized mutations in the single extended synaptotagmin (Esyt) ortholog in Drosophila melanogaster. Esyts are evolutionarily conserved ER proteins with Ca2+-sensing domains that have recently been shown to orchestrate membrane tethering and lipid exchange between the ER and plasma membrane. We first demonstrate that Esyt localizes to presynaptic ER structures at the neuromuscular junction. Next, we show that synaptic growth, structure, and homeostatic plasticity are surprisingly unperturbed at synapses lacking Esyt expression. However, neurotransmission is reduced in Esyt mutants, consistent with a presynaptic role in promoting neurotransmitter release. Finally, neuronal overexpression of Esyt enhances synaptic growth and the sustainment of the vesicle pool during intense activity, suggesting that increased Esyt levels may modulate the membrane trafficking and/or resting Ca2+ pathways that control synapse extension. Thus, we identify Esyt as a presynaptic ER protein that can promote neurotransmission and synaptic growth, revealing the first in vivo neuronal functions of this conserved gene family.

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Distinct and Cooperative Roles of amh and dmrt1 in Self-Renewal and Differentiation of Male Germ Cells in Zebrafish [Genetics of Sex]

November 2, 2017 - 8:33am

Spermatogenesis is a fundamental process in male reproductive biology and depends on precise balance between self-renewal and differentiation of male germ cells. However, the regulative factors for controlling the balance are poorly understood. In this study, we examined the roles of amh and dmrt1 in male germ cell development by generating their mutants with Crispr/Cas9 technology in zebrafish. Amh mutant zebrafish displayed a female-biased sex ratio, and both male and female amh mutants developed hypertrophic gonads due to uncontrolled proliferation and impaired differentiation of germ cells. A large number of proliferating spermatogonium-like cells were observed within testicular lobules of the amh-mutated testes, and they were demonstrated to be both Vasa- and PH3-positive. Moreover, the average number of Sycp3- and Vasa-positive cells in the amh mutants was significantly lower than in wild-type testes, suggesting a severely impaired differentiation of male germ cells. Conversely, all the dmrt1-mutated testes displayed severe testicular developmental defects and gradual loss of all Vasa-positive germ cells by inhibiting their self-renewal and inducing apoptosis. In addition, several germ cell and Sertoli cell marker genes were significantly downregulated, whereas a prominent increase of Insl3-positive Leydig cells was revealed by immunohistochemical analysis in the disorganized dmrt1-mutated testes. Our data suggest that amh might act as a guardian to control the balance between proliferation and differentiation of male germ cells, whereas dmrt1 might be required for the maintenance, self-renewal, and differentiation of male germ cells. Significantly, this study unravels novel functions of amh gene in fish.

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Ethanol Stimulates Locomotion via a G{alpha}s-Signaling Pathway in IL2 Neurons in Caenorhabditis elegans [Cellular Genetics]

November 2, 2017 - 8:33am

Alcohol is a potent pharmacological agent when consumed acutely at sufficient quantities and repeated overuse can lead to addiction and deleterious effects on health. Alcohol is thought to modulate neuronal function through low-affinity interactions with proteins, in particular with membrane channels and receptors. Paradoxically, alcohol acts as both a stimulant and a sedative. The exact molecular mechanisms for the acute effects of ethanol on neurons, as either a stimulant or a sedative, however remain unclear. We investigated the role that the heat shock transcription factor HSF-1 played in determining a stimulatory phenotype of Caenorhabditis elegans in response to physiologically relevant concentrations of ethanol (17 mM; 0.1% v/v). Using genetic techniques, we demonstrate that either RNA interference of hsf-1 or use of an hsf-1(sy441) mutant lacked the enhancement of locomotion in response to acute ethanol exposure evident in wild-type animals. We identify that the requirement for HSF-1 in this phenotype was IL2 neuron-specific and required the downstream expression of the α-crystallin ortholog HSP-16.48. Using a combination of pharmacology, optogenetics, and phenotypic analyses we determine that ethanol activates a Gαs-cAMP-protein kinase A signaling pathway in IL2 neurons to stimulate nematode locomotion. We further implicate the phosphorylation of a specific serine residue (Ser322) on the synaptic protein UNC-18 as an end point for the Gαs-dependent signaling pathway. These findings establish and characterize a distinct neurosensory cell signaling pathway that determines the stimulatory action of ethanol and identifies HSP-16.48 and HSF-1 as novel regulators of this pathway.

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Apico-basal Polarity Determinants Encoded by crumbs Genes Affect Ciliary Shaft Protein Composition, IFT Movement Dynamics, and Cilia Length [Developmental and Behavioral Genetics]

November 2, 2017 - 8:33am

One of the most obvious manifestations of polarity in epithelia is the subdivision of the cell surface by cell junctions into apical and basolateral domains. crumbs genes are among key regulators of this form of polarity. Loss of crumbs function disrupts the apical cell junction belt and crumbs overexpression expands the apical membrane size. Crumbs proteins contain a single transmembrane domain and localize to cell junction area at the apical surface of epithelia. In some tissues, they are also found in cilia. To test their role in ciliogenesis, we investigated mutant phenotypes of zebrafish crumbs genes. In zebrafish, mutations of three crumbs genes, oko meduzy/crb2a, crb3a, and crb2b, affect cilia length in a subset of tissues. In oko meduzy (ome), this is accompanied by accumulation of other Crumbs proteins in the ciliary compartment. Moreover, intraflagellar transport (IFT) particle components accumulate in the ciliary shaft of ome;crb3a double mutants. Consistent with the above, Crb3 knockdown in mammalian cells affects the dynamics of IFT particle movement. These findings reveal crumbs-dependent mechanisms that regulate the localization of ciliary proteins, including Crumbs proteins themselves, and show that crumbs genes modulate intraflagellar transport and cilia elongation.

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Body Shape and Coloration of Silkworm Larvae Are Influenced by a Novel Cuticular Protein [Developmental and Behavioral Genetics]

November 2, 2017 - 8:33am

The genetic basis of body shape and coloration patterns on caterpillars is often assumed to be regulated separately, but it is possible that common molecules affect both types of trait simultaneously. Here we examine the genetic basis of a spontaneous cuticle defect in silkworm, where larvae exhibit a bamboo-like body shape and decreased pigmentation. We performed linkage mapping and mutation screening to determine the gene product that affects body shape and coloration simultaneously. In these mutant larvae we identified a null mutation in BmorCPH24, a gene encoding a cuticular protein with low complexity sequence. Spatiotemporal expression analyses showed that BmorCPH24 is expressed in the larval epidermis postecdysis. RNAi-mediated knockdown and CRISPR/Cas9-mediated knockout of BmorCPH24 produced the abnormal body shape and the inhibited pigment typical of the mutant phenotype. In addition, our results showed that BmorCPH24 may be involved in the synthesis of endocuticle and its disruption-induced apoptosis of epidermal cells that accompanied the reduced expression of R&R-type larval cuticle protein genes and pigmentation gene Wnt1. Strikingly, BmorCPH24, a fast-evolving gene, has evolved a new function responsible for the assembly of silkworm larval cuticle and has evolved to be an indispensable factor maintaining the larval body shape and its coloration pattern. This is the first study to identify a molecule whose pleiotropic function affects the development of body shape and color patterns in insect larvae.

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Tra-2 Mediates Cross-Talk Between Sex Determination and Wing Polyphenism in Female Nilaparvata lugens [Developmental and Behavioral Genetics]

November 2, 2017 - 8:33am

Sexual dimorphism and wing polyphenism are important and evolutionarily conserved features of many insect species. In this article, we found a cross-talk linking sexual differentiation with wing polyphenism in the brown planthopper (BPH) Nilaparvata lugens (order: Hemiptera). Knockdown of the sex determination gene Transformer-2 in N. lugens (NlTra-2) in nymph caused females to develop into infertile pseudomales containing undeveloped ovaries. Whereas males treated with dsNlTra-2 exhibited normal morphology, but lost fertility. Knockdown of NlTra-2 in adult females (maternal RNAi) resulted in long-winged female offspring, indicating that maternal RNAi changed the wing morphs in female offspring. In addition, silencing of NlTra-2 down-regulated the expression of the forkhead transcription factor FoxO (NlFoxO), and simultaneously up-regulated the expression of phosphatidylinositol-3-OH kinase (PI(3)K)-protein kinase B (NlAkt), the two critical genes in the insulin signaling pathway. Furthermore, the long-winged effect caused by maternal dsNlTra-2 RNAi could be reversed by silencing of NlInR1 and NlAkt, leading to short-winged morphs. We propose that there is a cross-talk between the sexual differentiation and wing polyphenism pathways mediated by NlTra-2 during embryonic stages.

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Mitigating Mitochondrial Genome Erosion Without Recombination [Population and Evolutionary Genetics]

November 2, 2017 - 8:33am

Mitochondria are ATP-producing organelles of bacterial ancestry that played a key role in the origin and early evolution of complex eukaryotic cells. Most modern eukaryotes transmit mitochondrial genes uniparentally, often without recombination among genetically divergent organelles. While this asymmetric inheritance maintains the efficacy of purifying selection at the level of the cell, the absence of recombination could also make the genome susceptible to Muller’s ratchet. How mitochondria escape this irreversible defect accumulation is a fundamental unsolved question. Occasional paternal leakage could in principle promote recombination, but it would also compromise the purifying selection benefits of uniparental inheritance. We assess this tradeoff using a stochastic population–genetic model. In the absence of recombination, uniparental inheritance of freely-segregating genomes mitigates mutational erosion, while paternal leakage exacerbates the ratchet effect. Mitochondrial fusion–fission cycles ensure independent genome segregation, improving purifying selection. Paternal leakage provides opportunity for recombination to slow down the mutation accumulation, but always at a cost of increased steady-state mutation load. Our findings indicate that random segregation of mitochondrial genomes under uniparental inheritance can effectively combat the mutational meltdown, and that homologous recombination under paternal leakage might not be needed.

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