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

The mitochondrial genome (mtDNA) of Metazoa is a good model system for evolutionary genomic studies and the availability of more than 1000 sequences provides an almost unique opportunity to decode the mechanisms of genome evolution over a large phylogenetic range. In this paper, we review several structural features of the metazoan mtDNA, such as gene content, genome size, genome architecture and the new parameter of gene strand asymmetry in a phylogenetic framework. The data reviewed here show that: (1) the plasticity of Metazoa mtDNA is higher than previously thought and mainly due to variation in number and location of tRNA genes; (2) an exceptional trend towards stabilization of genomic features occurred in deuterostomes and was exacerbated in vertebrates, where gene content, genome architecture and gene strand asymmetry are almost invariant. Only tunicates exhibit a very high degree of genome variability comparable to that found outside deuterostomes. In order to analyse the genomic evolutionary process at short evolutionary distances, we have also compared mtDNAs of species belonging to the same genus: the variability observed in congeneric species significantly recapitulates the evolutionary dynamics observed at higher taxonomic ranks, especially for taxa showing high levels of genome plasticity and/or fast nucleotide substitution rates. Thus, the analysis of congeneric species promises to be a valuable approach for the assessment of the mtDNA evolutionary trend in poorly or not yet sampled metazoan groups.

/pdf/evolution-of-the-mitochondrial-genome-of-metazoa-as-4r6vaqyrza.pdf

Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species

Sequence variation in mitochondrial DNA (mtDNA) was traditionally considered to be selectively neutral. However, an accumulating body of evidence indicates that this assumption is invalid. Furthermore, recent advances indicate that mtDNA polymorphism can be maintained within populations via selection on the joint mitochondrial-nuclear genotype. Here, we review the latest findings that show mitochondrial and cytoplasmic genetic variation for life-history traits and fitness. We highlight the key importance of the mitochondrial-nuclear interaction as a unit of selection and discuss the consequences of mitochondrially encoded fitness effects on several key evolutionary processes. Our goal is to draw attention to the profound, yet neglected, influence of the mitochondrial genome on the fields of ecology and evolution.

https://www.cell.com/trends/ecology-evolution/pdf/S0169-5347(08)00251-6.pdf

Evolutionary implications of non-neutral mitochondrial genetic variation

Mitochondrial DNA (mtDNA) is a pivotal tool in molecular ecology, evolutionary and population genetics. The power of mtDNA analyses derives from a relatively high mutation rate and the apparent simplicity of mitochondrial inheritance (maternal, without recombination), which has simplified modelling population history compared to the analysis of nuclear DNA. However, in biology things are seldom simple, and advances in DNA sequencing and polymorphism detection technology have documented a growing list of exceptions to the central tenets of mitochondrial inheritance, with paternal leakage, heteroplasmy and recombination now all documented in multiple systems. The presence of paternal leakage, recombination and heteroplasmy can have substantial impact on analyses based on mtDNA, affecting phylogenetic and population genetic analyses, estimates of the coalescent and the myriad of other parameters that are dependent on such estimates. Here, we review our understanding of mtDNA inheritance, discuss how recent findings mean that established ideas may need to be re-evaluated, and we assess the implications of these new-found complications for molecular ecologists who have relied for decades on the assumption of a simpler mode of inheritance. We show how it is possible to account for recombination and heteroplasmy in evolutionary and population analyses, but that accurate estimates of the frequencies of biparental inheritance and recombination are needed. We also suggest how nonclonal inheritance of mtDNA could be exploited, to increase the ways in which mtDNA can be used in analyses.

/pdf/revealing-the-hidden-complexities-of-mtdna-inheritance-v11i49b03a.pdf

Revealing the hidden complexities of mtDNA inheritance

Maternal inheritance of mitochondrial DNA by diverse mechanisms to eliminate paternal mitochondrial DNA.

https://www.cell.com/trends/genetics/pdf/S0168-9525(07)00242-9.pdf

The unusual system of doubly uniparental inheritance of mtDNA : isn't one enough?

Doubly uniparental inheritance (DUI) of mitochondrial DNA in marine mussels (Mytiloida), freshwater mussels (Unionoida), and marine clams (Veneroida) is the only known exception to the general rule of strict maternal transmission of mtDNA in animals. DUI is characterized by the presence of gender-associated mitochondrial DNA lineages that are inherited through males (male-transmitted or M types) or females (female-transmitted or F types), respectively. This unusual system constitutes an excellent model for studying basic aspects of mitochondrial DNA inheritance and the evolution of mtDNA genomes in general. Here we compare published mitochondrial genomes of unionoid bivalve species with DUI, with an emphasis on characterizing unassigned regions, to identify regions of the F and M mtDNA genomes that could (i) play a role in replication or transcription of the mtDNA molecule and/or (ii) determine whether a genome will be transmitted via the female or the male gamete. Our results reveal the presence of one F-specific and one M-specific open reading frames (ORFs), and we hypothesize that they play a role in the transmission and/or gender-specific adaptive functions of the M and F mtDNA genomes in unionoid bivalves. Three major unassigned regions shared among all F and M unionoid genomes have also been identified, and our results indicate that (i) two of them are potential heavy-strand control regions (OH) for regulating replication and/or transcription and that (ii) multiple and potentially bidirectional light-strand origins of replication (OL) are present in unionoid F and M mitochondrial genomes. We propose that unassigned regions are the most promising candidate sequences in which to find regulatory and/or gender-specific sequences that could determine whether a mitochondrial genome will be maternally or paternally transmitted.

https://www.genetics.org/content/genetics/183/4/1575.full.pdf

Comparative Mitochondrial Genomics of Freshwater Mussels (Bivalvia: Unionoida) With Doubly Uniparental Inheritance of mtDNA: Gender-Specific Open Reading Frames and Putative Origins of Replication

Conclusions L’ensemble de ces travaux met en lumiere des proprietes nouvelles pour les composes impliques dans le metabolisme de la vitamine A. D’une part, le retinaldehyde limite le developpement adipocytaire et favorise la dissipation de l’energie, au moins chez le rongeur. D’autre part, la RBP4 apparait comme un signal dependant de l’utilisation de glucose et fortement associe a l’insulino-resistance. Bien que les relations potentielles entre le retinaldehyde et RBP4 restent encore a preciser, ces nouvelles decouvertes pourraient constituer une voie d’intervention prometteuse pour le developpement de strategies therapeutiques contre les maladies metaboliques de surcharge comme l’obesite et le diabete de type 2. ‡ Vitamin A, in the eye of the fat REFERENCES

/pdf/un-systeme-de-transmission-de-l-adn-mitochondrial-2r7akoo089.pdf

Un système de transmission de l’ADN mitochondrial sexuellement équitable

La dysphorie de genre réfère à une souffrance que l’individu ressent lorsque son sexe à la naissance ne correspond pas avec l’expression de son genre. La chirurgie d’affirmation de genre est une intervention qui va permettre de diminuer cette souffrance. Au Canada GrS Montréal est depuis 20 ans le seul centre dédié exclusivement à ce type de chirurgie. Par son expertise, la qualité des soins, une infrastructure de pointe, sa maison de convalescence, GrS Montréal reçoit des patient(es) de partout dans le monde. Cet article décrit les particularités de ce centre en mettant en perspective l’évolution de ce type de chirurgie. Gender dysphoria refers to the suffering an individual experiences when his or her sex at birth does not correspond to the expression of his or her gender. Gender-affirmation surgery is a procedure that can alleviate this suffering. For 20 years, GrS Montreal has been Canada's only center dedicated exclusively to this type of surgery. Thanks to its expertise, quality of care, state-of-the-art infrastructure and convalescent home, GrS Montreal receives patients from all over the world. This article describes the particularities of this center and puts into perspective the evolution of this type of surgery. 

Hélène Doucet Beaupré

Papers

The unusual system of doubly uniparental inheritance of mtDNA : isn't one enough?

Comparative Mitochondrial Genomics of Freshwater Mussels (Bivalvia: Unionoida) With Doubly Uniparental Inheritance of mtDNA: Gender-Specific Open Reading Frames and Putative Origins of Replication

Un système de transmission de l’ADN mitochondrial sexuellement équitable

GrS Montréal : un hôpital privé spécialisé en chirurgie d’affirmation de genre au Canada