Over the last three decades, mitochondrial DNA has been the most popular marker of molecular diversity, for a combination of technical ease-of-use considerations, and supposed biological and evolutionary properties of clonality, near-neutrality and clock-like nature of its substitution rate. Reviewing recent literature on the subject, we argue that mitochondrial DNA is not always clonal, far from neutrally evolving and certainly not clock-like, questioning its relevance as a witness of recent species and population history. We critically evaluate the usage of mitochondrial DNA for species delineation and identification. Finally, we note the great potential of accumulating mtDNA data for evolutionary and functional analysis of the mitochondrial genome.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-294X.2009.04380.x

Mitochondrial DNA as a marker of molecular diversity: a reappraisal

In nearly all eukaryotes, at least some individuals inherit mitochondrial and chloroplast genes from only one parent. There is no single mechanism of uniparental inheritance: organelle gene inheritance is blocked by a variety of mechanisms and at different stages of reproduction in different species. Frequent changes in the pattern of organelle gene inheritance during evolution suggest that it is subject to varying selective pressures. Organelle genes often fail to recombine even when inherited biparentally; consequently, their inheritance is asexual. Sexual reproduction is apparently less important for genes in organelles than for nuclear genes, probably because there are fewer of them. As a result organelle sex can be lost because of selection for special reproductive features such as oogamy or because uniparental inheritance reduces the spread of cytoplasmic parasites and selfish organelle DNA.

https://www.pnas.org/content/pnas/92/25/11331.full.pdf

Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution.

▪ Abstract The inheritance of mitochondrial and chloroplast genes differs from that of nuclear genes in showing vegetative segregation, uniparental inheritance, intracellular selection, and reduced recombination. Vegetative segregation and some cases of uniparental inheritance are due to stochastic replication and partitioning of organelle genomes. The rate and pattern of vegetative segregation depend partly on the numbers of genomes and of organelles per cell, but more importantly on the extent to which genomes are shared between organelles, their distribution in the cell, the variance in number of replications per molecule, and the variance in numerical and genotypic partitioning of organelles and genomes. Most of these parameters are unknown for most organisms, but a simple binomial probability model using the effective number of genomes is a useful substitute. Studies using new cytological, molecular, and genetic methods are shedding some light on the processes involved in segregation, and also on the...

THE INHERITANCE OF GENES IN MITOCHONDRIA AND CHLOROPLASTS: Laws, Mechanisms,

Malignant neoplasms that develop in 12 recessive-lethal, larval mutants of Drosophila melanogaster are discussed. These mutations affect the adult optic neuroblasts and ganglion-mother cells in the larval brain, the imaginal discs, and the hematopoietic organs. The malignant neoplasms exhibit fast, autonomous growth, loss of the capacity for differentiation, increased mobility and invasiveness, lethality in situ and after transplantation, and histological, fine structural, and karyotypic abnormalities. Intermediate neoplasms are also found. These combine both benign and malignant qualities. They grow in a noninvasive, compact fashion, typical of benign tumors, yet they also exhibit malignant qualities such as fast, autonomous, and lethal growth, loss of differentiation capacity, changes in cellular morphology, and lethal growth after transplantation into wild-type hosts. Thus Drosophila and vertebrate neoplasms show striking similarities.

Malignant neoplasms of genetic origin in Drosophila melanogaster

Among all the areas of biological science, genetics is one of the most beautifully exact and formal in its structure. The subject is built upon a framework of precisely formulated laws of great generality, and most of those laws are firmly grounded in mechanistic explanations in terms of the behavior of cells, chromosomes, and molecules. One aspect of heredity has largely resisted such treatment: the study of organelle genes, which are located inside mitochondria or chloroplasts and consequently are inherited via the cytoplasm. The first cases of cytoplasmic inheritance, later shown to involve plastid genes, were discovered by Correns (1909) and Baur (1909) just a few years after the rediscovery of the Mendelian laws, which describe the inheritance of nuclear genes. The next 50 years saw the discovery of more instances of plastid mutants in higher plants (reviewed by Kirk and Tilney-Bassett 1967) and in algae (reviewed by Sager 1972), and the first cases of mitochondrial gene mutants (Ephrussi et al. 1949, Mitchell and Mitchell 1952). But the investigation of these phenomena lagged far behind that of the more numerous and more easily studied nuclear genes; some geneticists were reluctant to believe in the existence, let alone the importance, of genes in the cytoplasm. Then, in the early 1960's, the discovery of DNA in plastids (Chun et al. 1963, Ris and Plaut 1962, Sager and Ishida 1963) and in mitochondria (Luck and Reich 1964, Nass and Nass 1963, Schatz et al. 1964) made the study of genes in these organelles respectable, and the study of their unique DNA's has virtually become a scientific bandwagon. Nevertheless, scientists are still far from a clear

The Inheritance of Genes in Mitochondria and Chloroplasts

The spermatozoa of Ascidia nigra contain only one mitochondrion. Phase contrast and electron microscopical evidence is presented showing that the spermatozoon loses its mitochondrion before it enters the perivitelline space. Thus, in these organisms, the paternal mitochondrion plays no role in the development of the zygote and cannot contribute mitochondrial DNA to the genetic repertory of the zygote.

Fertilization in tunicates: loss of the paternal mitochondrion prior to sperm entry.

The fine structure of male genital disks of Drosophila between the late second larval instar and early pupal stage is described. Two major developmental changes were observed. One, the incidence of rough endoplasmic reticulum increases around the time of puparium formation. Two, the incidence of microvilli increases around the time of the moult from the second to the third larval instar.

The fine structure of the male Drosophila genital disk during late larval and early pupal development.

The ultrastructure of the spermatozoon of Ascidia nigra is described. The head of this sperm contains an elongated nucleus flanked and surrounded by a single large mitochondrion. No other mitochondria are present. An acrosome is seen to extend over a large portion of the nucleus. The tail shows the typical 9 + 2 arrangement of fibrils, and in some region carries fins.

The fine structure of the sperm of a tunicate, Ascidia nigra.

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Fertilization in tunicates: loss of the paternal mitochondrion prior to sperm entry.

The fine structure of the male Drosophila genital disk during late larval and early pupal development.

The fine structure of the sperm of a tunicate, Ascidia nigra.