Paternal Leakage Research Articles

Mitogenomic analysis of a 50-generation chicken pedigree reveals a rapid rate of mitochondrial evolution and evidence for paternal mtDNA inheritance.

Mitochondrial genomes represent a valuable source of data for evolutionary research, but studies of their short-term evolution have typically been limited to invertebrates, humans and laboratory organisms. Here we present a detailed study of 12 mitochondrial genomes that span a total of 385 transmissions in a well-documented 50-generation pedigree in which two lineages of chickens were selected for low and high juvenile body weight. These data allowed us to test the hypothesis of time-dependent evolutionary rates and the assumption of strict maternal mitochondrial transmission, and to investigate the role of mitochondrial mutations in determining phenotype. The identification of a non-synonymous mutation in ND4L and a synonymous mutation in CYTB, both novel mutations in Gallus, allowed us to estimate a molecular rate of 3.13 × 10−7 mutations/site/year (95% confidence interval 3.75 × 10−8–1.12 × 10−6). This is substantially higher than avian rate estimates based upon fossil calibrations. Ascertaining which of the two novel mutations was present in an additional 49 individuals also revealed an instance of paternal inheritance of mtDNA. Lastly, an association analysis demonstrated that neither of the point mutations was strongly associated with the phenotypic differences between the two selection lines. Together, these observations reveal the highly dynamic nature of mitochondrial evolution over short time periods.

Persistence and Protection of Mitochondrial DNA in the Generative Cell of Cucumber is Consistent with its Paternal Transmission.

Plants predominantly show maternal transmission of mitochondrial DNA (mtDNA). One known exception is cucumber, in which the mtDNA is paternally inherited. However, the mechanisms regulating this unique mode of transmission are unclear. Here we monitored the amounts of mtDNA throughout the development of cucumber microspores into pollen and observed that mtDNA decreases in the vegetative cell, but persists in the generative cell that ultimately produces the sperm cells. We characterized the cucumber homolog (CsDPD1) of the Arabidopsis gene defective in pollen organelle DNA degradation 1 (AtDPD1), which plays a direct role in mtDNA degradation. CsDPD1 rescued an Arabidopsis AtDPD1 mutant, indicating the same function in both plants. Expression of CsDPD1 coincided with the decrease of mtDNA in pollen, except in the generative cell where both the expression of CsDPD1 and mtDNA levels remained high. Our cytological results confirmed that the persistence of mtDNA in the cucumber generative cell is consistent with its paternal transmission. Our molecular analyses suggest that protection of mtDNA in the generative cell may be the critical factor for paternal mtDNA transmission, rather than mtDNA degradation mediated by CsDPD1. Taken together, these findings indicate that a mechanism may protect paternal mtDNA from degradation and is likely to be the genetic basis of paternal mtDNA transmission.

Atypical mitochondrial inheritance patterns in eukaryotes.

Mitochondrial DNA (mtDNA) is predominantly maternally inherited in eukaryotes. Diverse molecular mechanisms underlying the phenomenon of strict maternal inheritance (SMI) of mtDNA have been described, but the evolutionary forces responsible for its predominance in eukaryotes remain to be elucidated. Exceptions to SMI have been reported in diverse eukaryotic taxa, leading to the prediction that several distinct molecular mechanisms controlling mtDNA transmission are present among the eukaryotes. We propose that these mechanisms will be better understood by studying the deviations from the predominating pattern of SMI. This minireview summarizes studies on eukaryote species with unusual or rare mitochondrial inheritance patterns, i.e., other than the predominant SMI pattern, such as maternal inheritance of stable heteroplasmy, paternal leakage of mtDNA, biparental and strictly paternal inheritance, and doubly uniparental inheritance of mtDNA. The potential genes and mechanisms involved in controlling mitochondrial inheritance in these organisms are discussed. The linkage between mitochondrial inheritance and sex determination is also discussed, given that the atypical systems of mtDNA inheritance examined in this minireview are frequently found in organisms with uncommon sexual systems such as gynodioecy, monoecy, or andromonoecy. The potential of deviations from SMI for facilitating a better understanding of a number of fundamental questions in biology, such as the evolution of mtDNA inheritance, the coevolution of nuclear and mitochondrial genomes, and, perhaps, the role of mitochondria in sex determination, is considerable.

Extensive Mitochondrial Heteroplasmy in Natural Populations of a Resurging Human Pest, the Bed Bug (Hemiptera: Cimicidae).

Homoplasmy, the occurrence of a single mitochondrial DNA haplotype within an individual, has been the accepted condition across most organisms in the animal kingdom. In recent years, a number of exceptions to this rule have been reported, largely due to the ease with which single nucleotide polymorphisms can be detected. Evidence of heteroplasmy-two or more mitochondrial variants within a single individual-has now been documented in a number of invertebrates; however, when present, heteroplasmy usually occurs at low frequencies both within individuals and within populations. The implications of heteroplasmy may be far reaching, both to the individual in relation to its health and fitness, and when considering the evolutionary dynamics of populations. We present novel evidence for frequent mtDNA heteroplasmy in the bed bug, Cimex lectularius L. (Hemiptera: Cimicidae). Our findings show that heteroplasmy is common, with 5 of 29 (17%) populations screened exhibiting two mitochondrial variants in a ∼1:2 ratio within each individual. We hypothesize that the mechanism underlying heteroplasmy in bed bugs is paternal leakage because some haplotypes were shared among unrelated populations and no evidence for nuclear mitochondrial DNA sequences was detected.

Keeping in shape the dogma of mitochondrial DNA maternal inheritance.

It is textbook knowledge that the small multicopy mitochondrial genome (mtDNA) is maternally inherited in humans and mammals [1,2]. The uniparental mtDNA inheritance applies to most eukaryotic organisms, including animals exhibiting the doubly uniparental inheritance, such as the bivalve mollusks [3,4]. Occurrence of paternal mtDNA transmission has also been documented [5–7], and doubts on strict maternal inheritance in humans have been raised [8,9]. The best-documented case of paternal mtDNA inheritance was in a patient carrying a pathogenic mtDNA mutation [9], never replicated in following studies of patients with mitochondrial diseases due to various mtDNA defects [10–12]. The sperm mitochondria enter the oocyte during fertilization in mammals [13], but paternal mitochondria and mtDNA disappear at the initial cell divisions of the embryo in a stringently species-specific fashion [14]. In fact, the failure to efficiently eliminate paternal mtDNA from different species intercrosses [14,15] explains some of the cases of paternally inherited mtDNA [5]. Furthermore, recognition and targeted elimination of exogenous mtDNA entering the oocyte seems restricted to sperm mtDNA, not occurring with liver mtDNA, thus also displaying tissue specificity [16]. The way by which paternal mtDNA inheritance fails to occur in humans remains elusive, and it appears that several mechanisms have coevolved to avoid paternal mtDNA contribution to the embryo [17]. It has been observed that sperm mitochondria are ubiquitinated, suggestive of an “active elimination model” for paternal mtDNA [14], which may occur through different routes, such as proteosomal or lysosomal pathways [14,17]. Autophagy has been recently highlighted as the mechanism for paternal mtDNA elimination in Caenorhabditis elegans [18,19]. This was not observed in mice, for which elimination of mtDNA from prefertilization sperm and uneven persistence of paternal mtDNA in the embryo raised the possibility of a passive “dilution model” of disproportionate paternal versus maternal mtDNAs in mammals [20]. The consequent leakage of paternal mtDNA in the newborn may have remained “undetected” by the standard sequencing approaches.

Female-dependent transmission of paternal mtDNA is a shared feature of bivalve species with doubly uniparental inheritance (DUI) of mitochondrial DNA

Several species from a number of bivalve molluscan families are known to have a paternally transmitted mitochondrial genome, along with the standard maternally transmitted one. The main characteristic of the phenomenon, known as doubly uniparental inheritance (DUI), is the coupling of sex and mtDNA inheritance: males receive both genomes but transmit only the paternal to their progeny; females either do not have the paternal genome or, if they do, they do not transmit it to their progeny. In the families Mytilidae and Veneridae, both of which have DUI, a female individual is either female-biased (it produces only, or nearly so, female progeny), male-biased (it produces mainly male progeny) or non-biased (it produces both genders in intermediate frequencies). Here we present evidence for a same pattern in the freshwater mussel, Unio delphinus (Unionidae). These results suggest that the maternal control of whether a fertilized egg will develop into a male or a female individual (and the associated feature of whether it will inherited or not inherit the paternal mtDNA) is a general characteristic of species with DUI.

Can paternal leakage maintain sexually antagonistic polymorphism in the cytoplasm?

A growing number of studies in multicellular organisms highlight low or moderate frequencies of paternal transmission of cytoplasmic organelles, including both mitochondria and chloroplasts. It is well established that strict maternal inheritance is selectively blind to cytoplasmic elements that are deleterious to males – ’mother's curse’. But it is not known how sensitive this conclusion is to slight levels of paternal cytoplasmic leakage. We assess the scope for polymorphism when individuals bear multiple cytoplasmic alleles in the presence of paternal leakage, bottlenecks and recurrent mutation. When fitness interactions among cytoplasmic elements within an individual are additive, we find that sexually antagonistic polymorphism is restricted to cases of strong selection on males. However, when fitness interactions among cytoplasmic elements are nonlinear, much more extensive polymorphism can be supported in the cytoplasm. In particular, mitochondrial mutants that have strong beneficial fitness effects in males and weak deleterious fitness effects in females when rare (i.e. ’reverse dominance’) are strongly favoured under paternal leakage. We discuss how such epistasis could arise through preferential segregation of mitochondria in sex-specific somatic tissues. Our analysis shows how paternal leakage can dampen the evolution of deleterious male effects associated with predominant maternal inheritance of cytoplasm, potentially explaining why ’mother's curse’ is less pervasive than predicted by earlier work.

Do gynogenetic species escape evolving enemies?

Gynogenetic organisms are asexual females of one species that require sperm from males of another species to initiate reproduction (but except in rare instances of ‘paternal leakage’, those sperm do not contribute to the genetic make-up of the gynogens’ offspring). Gynogenetic organisms seem to combine disadvantages of both sexual and asexual reproductive strategies (e.g., mating costs, reduced genetic diversity). We borrowed logic from the Red Queen Hypothesis (RQH) to help explain the persistence of gynogenetic species in nature, which is a paradox. The RQH is the most oft-cited explanation for the maintenance of sex. It states that evolving enemies generate a constantly changing environment, which provides the conditions that make sex advantageous. Under this scenario, asexual organisms cannot evolve fast enough to ‘keep up’ with co-evolving parasites and disease causing organisms, and ultimately show reduced fitness compared to sexual individuals. The RQH tends to view asexuality generally, ignoring important nuance in nature like gynogenetic species in mixed assemblages with closely related sexual species. We outline tests of the argument that sperm dependency prevents asexual gynogens from outcompeting sexuals in mixed species assemblages and that this further allows gynogens to escape evolving enemies.

Different degree of paternal mtDNA leakage between male and female progeny in interspecific Drosophila crosses.

Maternal transmission of mitochondrial DNA (mtDNA) in animals is thought to prevent the spread of selfish deleterious mtDNA mutations in the population. Various mechanisms have been evolved independently to prevent the entry of sperm mitochondria in the embryo. However, the increasing number of instances of paternal mtDNA leakage suggests that these mechanisms are not very effective. The destruction of sperm mitochondria in mammalian embryos is mediated by nuclear factors. Also, the destruction of paternal mitochondria in intraspecific crosses is more effective than in interspecific ones. These observations have led to the hypothesis that leakage of paternal mtDNA (and consequently mtDNA recombination owing to ensuing heteroplasmy) might be more common in inter- than in intraspecific crosses and that it should increase with phylogenetic distance of hybridizing species. We checked paternal leakage in inter- and intraspecific crosses in Drosophila and found little evidence for this hypothesis. In addition, we have observed a higher level of leakage among male than among female progeny from the same cross. This is the first report of sex-specific leakage of paternal mtDNA. It suggests that paternal mtDNA leakage might not be a stochastic result of an error-prone mechanism, but rather, it may be under complex genetic control.

Accelerated evolution of the mitochondrial genome in an alloplasmic line of durum wheat

BackgroundWheat is an excellent plant species for nuclear mitochondrial interaction studies due to availability of large collection of alloplasmic lines. These lines exhibit different vegetative and physiological properties than their parents. To investigate the level of sequence changes introduced into the mitochondrial genome under the alloplasmic condition, three mitochondrial genomes of the Triticum-Aegilops species were sequenced: 1) durum alloplasmic line with the Ae. longissima cytoplasm that carries the T. turgidum nucleus designated as (lo) durum, 2) the cytoplasmic donor line, and 3) the nuclear donor line.ResultsThe mitochondrial genome of the T. turgidum was 451,678 bp in length with high structural and nucleotide identity to the previously characterized T. aestivum genome. The assembled mitochondrial genome of the (lo) durum and the Ae. longissima were 431,959 bp and 399,005 bp in size, respectively. The high sequence coverage for all three genomes allowed analysis of heteroplasmy within each genome. The mitochondrial genome structure in the alloplasmic line was genetically distant from both maternal and paternal genomes. The alloplasmic durum and the Ae. longissima carry the same versions of atp6, nad6, rps19-p, cob and cox2 exon 2 which are different from the T. turgidum parent. Evidence of paternal leakage was also observed by analyzing nad9 and orf359 among all three lines. Nucleotide search identified a number of open reading frames, of which 27 were specific to the (lo) durum line.ConclusionsSeveral heteroplasmic regions were observed within genes and intergenic regions of the mitochondrial genomes of all three lines. The number of rearrangements and nucleotide changes in the mitochondrial genome of the alloplasmic line that have occurred in less than half a century was significant considering the high sequence conservation between the T. turgidum and the T. aestivum that diverged from each other 10,000 years ago. We showed that the changes in genes were not limited to paternal leakage but were sufficiently significant to suggest that other mechanisms, such as recombination and mutation, were responsible. The newly formed ORFs, differences in gene sequences and copy numbers, heteroplasmy, and substoichiometric changes show the potential of the alloplasmic condition to accelerate evolution towards forming new mitochondrial genomes.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-67) contains supplementary material, which is available to authorized users.

Paternal leakage, heteroplasmy, and the evolution of plant mitochondrial genomes

Plant mitochondrial genomes are usually transmitted to the progeny from the maternal parent. However, cases of paternal transmission are known and are perhaps more common than once thought. This review will consider recent evidence, both direct and indirect, of paternal transmission (leakage) of the mitochondrial genome of seed plants, especially in natural populations, and how this can result in offspring that carry a mixture of maternally and paternally derived copies of the genome; a type of heteroplasmy. It will further consider how this heteroplasmy facilitates recombination between genetically distinct partners; a process that can enhance mitochondrial genotypic diversity. This will then form the basis for a discussion of five evolutionary questions that arise from these observations. Questions include how plant mitochondrial genome evolution can be placed on a sexual to asexual continuum, whether cytoplasmic male sterility (CMS) facilitates the evolution of paternal leakage, whether paternal leakage is more likely in populations undergoing admixture, how leakage influences patterns of gene flow, and whether heteroplasmy occurs in natural populations at a frequency greater than predicted by crossing experiments. It is proposed that each of these questions offers fertile ground for future research on a diversity of plant species.

Hybridisation, paternal leakage and mitochondrial DNA linearization in three anomalous fish (Scombridae)

Using mitochondrial DNA for species identification and population studies assumes that the genome is maternally inherited, circular, located in the cytoplasm and lacks recombination. This study explores the mitochondrial genomes of three anomalous mackerel. Complete mitochondrial genome sequencing plus nuclear microsatellite genotyping of these fish identified them as Scomberomorus munroi (spotted mackerel). Unlike normal S. munroi, these three fish also contained different linear, mitochondrial genomes of Scomberomorus semifasciatus (grey mackerel). The results are best explained by hybridisation, paternal leakage and mitochondrial DNA linearization. This unusual observation may provide an explanation for mtDNA outliers in animal population studies.

Transmission of human mitochondrial DNA along the paternal lineage in transmitochondrial mice

Previously we obtained heteroplasmic mice carrying murine and human mitochondrial DNA (mtDNA). Even the fourth generation of such mice had human mtDNA in their organs, hence, they were used to study the possibility of paternal mtDNA transmission. A lineage was obtained in which human mtDNA was transmitted by males to the progeny in four successive generations. This is the first observation of such a continuous paternal transmission of mtDNA. Persistence of paternal mtDNA in several successive generations of animals suggests that mechanisms aimed at elimination of paternally inherited mtDNA species are not as strict as has been postulated.

Mitochondrial genome is paternally inherited in Cucumis allotetraploid (C. × hytivus) derived by interspecific hybridization

Paternal transmission of the mitochondrial (mt) genome in cucumber (Cucumis sativus L.) was revealed previously using intraspecific crosses. The present study reports the first paternal transmission of mtDNA observed between Cucumis species. Mitochondrial primers specific to nad1, cob, and nad7 were used to amplify the DNAs from the female parent (C. hystrix), male parent (C. sativus) and the allotetraploid (C.×hytivus) derived the interspecific hybridization. By sequence alignment, we found that the explicit nucleotide polymorphisms of the allotetraploid were all inherited from male parent, C. sativus. Similar experiment with chloroplast (cp) genome was conducted and the results showed that while mtDNA was paternally inherited, cpDNA was still maternally inherited between Cucumis species. This work provides novel evidence of paternal transmission of the mitochondrial genome between plant species and lays the foundation for further research on the genetic mechanism of mitochondrial transmission in Cucumis.

A possible breakage of linkage disequilibrium between mitochondrial and chloroplast genomes during Emmer and Dinkel wheat evolution

In wheat (Triticum) and Aegilops, chloroplast and mitochondrial genomes have been studied for over three decades to clarify the phylogenetic relationships among species, and most of the maternal lineages of polyploid species have been clarified. Mitochondrial genomes of Emmer (tetraploid with nuclear genome AABB) and Dinkel (hexaploid with AABBDD) wheat are classified into two different types, VIIa and VIIb, by the presence-absence of the third largest HindIII fragment (named H3) in the mitochondrial DNA. Although the mitochondrial genome in the genera often provides useful information to clarify the phylogenetic relationship among closely related species, the phylogenetic significance of this dimorphism has yet not been clarified. In this study, to facilitate analysis using a large number of accessions, a sequence characterized amplified region (SCAR) marker that distinguishes the type VIIb mitochondrial genome from type VIIa was first developed. Mitochondrial genome type was determined for each of 30 accessions of wild and cultivated Emmer wheat and 25 accessions of Dinkel wheat. The mitochondrial genome type for each accession was compared with the plastogroup that had been determined using chloroplast microsatellite markers. Unexpectedly, the distribution of mitochondrial genome type was not in accordance with that of the plastogroups, suggesting occasional paternal leakage of either the mitochondrial or chloroplast genome during speciation and differentiation of Emmer and Dinkel wheat. An alternative possibility that substoichiometric shifting is involved in the observed dimorphism of the mitochondrial genome is also discussed.

Extensive paternal mtDNA leakage in natural populations of Drosophila melanogaster

Strict maternal inheritance is considered a hallmark of animal mtDNA. Although recent reports suggest that paternal leakage occurs in a broad range of species, it is still considered an exceptionally rare event. To evaluate the impact of paternal leakage on the evolution of mtDNA, it is essential to reliably estimate the frequency of paternal leakage in natural populations. Using allele-specific real-time quantitative PCR (RT-qPCR), we show that heteroplasmy is common in natural populations with at least 14% of the individuals carrying multiple mitochondrial haplotypes. However, the average frequency of the minor mtDNA haplotype is low (0.8%), which suggests that this pervasive heteroplasmy has not been noticed before due to a lack of power in sequencing surveys. Based on the distribution of mtDNA haplotypes in the offspring of heteroplasmic mothers, we found no evidence for strong selection against one of the haplotypes. We estimated that the rate of paternal leakage is 6% and that at least 100 generations are required for complete sorting of mtDNA haplotypes. Despite the high proportion of heteroplasmic individuals in natural populations, we found no evidence for recombination between mtDNA molecules, suggesting that either recombination is rare or recombinant haplotypes are counter-selected. Our results indicate that evolutionary studies using mtDNA as a marker might be biased by paternal leakage in this species.

Mitochondrial DNA- a Tool for Phylogenetic and Biodiversity Search in Equines

It is imperative to assess the maternal lineage in order to achieve a broad picture of evolution, phylogenetic and genetic biodiversity within and among different breeds of livestock. In recent past, there has been a considerable advancement in sequencing of complete mammalian mtDNA molecules and their analysis. Most of the studies have focused on the mitochondrial D-loop region, the most variable part of mtDNA due to increased substitution rate than in the rest of the mtDNA genome which serves as a better genetic marker to assess the diversity. Mitochondrial DNA (mtDNA) possesses several favorable characteristics, including large quantity in the cell, small genome size, haploid, maternal inheritance with extremely low probability of paternal leakage, higher mutation rate than nuclear DNA, and amenable to change mainly through mutation rather than recombination. All these features make mtDNA a useful and one of the most frequently used markers in molecular systematic and has been widely employed to address questions of genetic diversity, population structure and population evolution of animals including equines. Many native breeds of horses as well as ponies were assessed for their genetic diversity and ancestry on the basis of studies on mitochondrial DNA to address the questions of evolution along with breed development and conservation.

Site heteroplasmy in the mitochondrial cytochrome b gene of the sterlet sturgeon Acipenser ruthenus

Sturgeons are fish species with a complex biology. They are also characterized by complex aspects including polyploidization and easiness of hybridization. As with most of the Ponto-Caspian sturgeons, the populations of Acipenser ruthenus from the Danube have declined drastically during the last decades. This is the first report on mitochondrial point heteroplasmy in the cytochrome b gene of this species. The 1141 bp sequence of the cytb gene in wild sterlet sturgeon individuals from the Lower Danube was determined, and site heteroplasmy evidenced in three of the 30 specimens collected. Two nucleotide sequences were identified in these heteroplasmic individuals. The majority of the heteroplasmic sites are synonymous and do not modify the sequence of amino acids in cytochrome B protein. To date, several cases of point heteroplasmy have been reported in animals, mostly due to paternal leakage of mtDNA. The presence of specific point heteroplasmic sites might be interesting for a possible correlation with genetically distinct groups in the Danube River.

Paternal transmission of mitochondrial DNA as an integral part of mitochondrial inheritance in metapopulations of Drosophila simulans

Maternal inheritance is one of the hallmarks of animal mitochondrial DNA (mtDNA) and central to its success as a molecular marker. This mode of inheritance and subsequent lack of heterologous recombination allows us to retrace evolutionary relationships unambiguously down the matriline and without the confounding effects of recombinant genetic information. Accumulating evidence of biparental inheritance of mtDNA (paternal leakage), however, challenges our current understanding of how this molecule is inherited. Here, using Drosophila simulans collected from an East African metapopulation exhibiting recurring mitochondrial heteroplasmy, we conducted single fly matings and screened F1 offspring for the presence of paternal mtDNA using allele-specific PCR assays (AS-PCR). In all, 27 out of 4092 offspring were identified as harboring paternal mtDNA, suggesting a frequency of 0.66% paternal leakage in this species. Our findings strongly suggest that recurring mtDNA heteroplasmy as observed in natural populations of Drosophila simulans is most likely caused by repeated paternal leakage. Our findings further suggest that this phenomenon to potentially be an integral part of mtDNA inheritance in these populations and consequently of significance for mtDNA as a molecular marker.

Paternal leakage of mitochondrial DNA in experimental crosses of populations of the potato cyst nematode Globodera pallida

Animal mtDNA is typically assumed to be maternally inherited. Paternal mtDNA has been shown to be excluded from entering the egg or eliminated post-fertilization in several animals. However, in the contact zones of hybridizing species and populations, the reproductive barriers between hybridizing organisms may not be as efficient at preventing paternal mtDNA inheritance, resulting in paternal leakage. We assessed paternal mtDNA leakage in experimental crosses of populations of a cyst-forming nematode, Globodera pallida. A UK population, Lindley, was crossed with two South American populations, P5A and P4A. Hybridization of these populations was supported by evidence of nuclear DNA from both the maternal and paternal populations in the progeny. To assess paternal mtDNA leakage, a ~3.4kb non-coding mtDNA region was analyzed in the parental populations and in the progeny. Paternal mtDNA was evident in the progeny of both crosses involving populations P5A and P4A. Further, paternal mtDNA replaced the maternal mtDNA in 22 and 40% of the hybrid cysts from these crosses, respectively. These results indicate that under appropriate conditions, paternal leakage occurs in the mtDNA of parasitic nematodes, and supports the hypothesis that hybrid zones facilitate paternal leakage. Thus, assumptions of strictly maternal mtDNA inheritance may be frequently violated, particularly when divergent populations interbreed.