Mitochondrial DNA variation in North American populations of Daphnia obtusa: continentalism or cryptic endemism?

The morphological stasis of many freshwater crustaceans has resulted in the prior delineation of cosmopolitan species and has been explained by their capacity for long-distance dispersal. This study examines the phylogeography of Daphnia obtusa, a cladoceran thought to be widespread in North America. However, sequence variation of the mitochondrial cytochrome c oxidase subunit I gene indicates that this taxon is composed of two morphologically cryptic species, designated D. obtusa NA1 and NA2. NA2 is restricted to the east, whereas NA1 is broadly distributed across the United States, and is subdivided into four phylogroups that show weak genetic differentiation over broad geographical areas, which likely reflects recent long-distance dispersal. The current distributions of the four phylogroups in NA1 can be explained by recent range expansion from different refugia following the last Pleistocene glacial advance. Interestingly, the mitochondrial phylogroups identified in this study do not correspond to lineages detected in a previous allozyme analysis. However, the latter groups are associated with a habitat shift suggesting that natural selection may have played a role in their divergence. The results of this and previous studies illustrate the complicated biogeographical history of freshwater cladocerans.     

D-loop mutations in mitochondrial DNA: link with mitochondrial DNA depletion?

Clinical presentation of the patients with mitochondrial DNA depletion is quite diverse and is suggestive of genetic heterogeneity. Autosomal recessive inheritance of the disease appears likely, thus implying the nuclear origin of the disease. This has been demonstrated recently in large families with neonatal presentation of the disease. Here, we report upon a family with one child having a late-onset disease associated with severe mitochondrial DNA depletion. The presence of mitochondrial alterations in the muscle of the patient's mother prompted us to extensively analyse the mitochondrial DNA in the family. We found mitochondrial DNA multiple deletions, but also three heteroplasmic point mutations of the D-loop region, two of which (T119C and T408A) affect conserved regions involved in the mtDNA replication process. These mutations were non-randomly distributed in the maternal lineage and, for one of them, among single muscle fibres. Involvement of the mitochondrial DNA in its own depletion appears therefore possible. It may act in close relationship with a hypothetical modified nuclear factor.     

Recombination in human mitochondrial DNA?

The possibility of recombination in human mitochondrial DNA (mtDNA) has been hotly debated over the last few years. In this study, a general model of recombination in circular molecules is developed and applied to a recently published African sample (n = 21) of complete mtDNA sequences. It is shown that the power of correlation measures to detect recombination in circular molecules can be vanishingly small and that the data are consistent with the given model and no recombination only if the overall heterogeneity in mutation rate is <0.09.     

Does the Platanthera dilatata (Orchidaceae) complex contain cryptic species or continuously variable populations?

Floral phenotypic traits are expected to reflect evolutionary changes and are used as a reliable basis for species delimitation. However, when traits overlap among populations of newly emerging species, this confounds identification of evolutionarily distinct lineages and reduces taxonomic stability. In this study, we quantified variation in ten floral traits and plastid DNA sequences across 26 populations of Platanthera dilatata (Orchidaceae) in North America to determine geographic structure among populations and to evaluate support for three varieties recognized in the current taxonomy. k-means clustering analysis, in the absence of a priori designation of groups, indicated two morphologically distinct groups. Spur length was the most distinctive character between groups. The group containing larger flowers with longer spurs corresponds to the var. leucostachys and most samples in this group are from western North America. The vars. albiflora and dilatata could not be distinguished within the second group, which exhibited flowers with short to intermediate spurs and include samples from eastern and western North America. Morphological variation in P. dilatata may reflect pollinator-mediated selection, particularly in spur length, which is known to vary in association with pollinators across Platanthera. Significant genetic divergence was observed between the two groups (F _ST = 0.15; P ≤ 0.001), but we did not find corresponding phylogenetic structure, which may reflect recent divergence and retention of ancestral polymorphisms. Based on these results, we suggest preserving the current intraspecific taxonomy until further studies determine the origin of floral variation and the extent of gene flow between morphologically divergent populations.     

The inheritance of mitochondrial DNA heteroplasmy: random drift, selection or both?

The mammalian mitochondrial genome (mtDNA) is a small double-stranded DNA molecule that is exclusively transmitted down the maternal line. Pathogenic mtDNA mutations are usually heteroplasmic, with a mixture of mutant and wild-type mtDNA within the same organism. A woman harbouring one of these mutations transmits a variable amount of mutant mtDNA to each offspring. This can result in a healthy child or an infant with a devastating and fatal neurological disorder. Understanding the biological basis of this uncertainty is one of the principal challenges facing scientists and clinicians in the field of mitochondrial genetics.     

Are mitochondrial lineages,mitochondrial lysis and respiration rate associated with phosphine susceptibility in the maize weevil Sitophilus zeamais?

Phosphine is the most widely used fumigant with ever‐growing problems of phosphine resistance among insect pests of stored products. One such insect is the maize weevil Sitophilus zeamais, a key pest of stored cereals. Despite its importance as a fumigant, the mechanisms of phosphine toxicity and resistance remain unclear, although the mitochondrion is broadly recognised as its site of action. Here we explored the phosphine susceptibility of maize weevil populations and its association with insect respiration rate, and we tested the association of phosphine susceptibility with the mitochondrial lineages from the field populations studied. We also assessed the action of phosphine in the degradation of mitochondria from muscle cells. Survival under phosphine treatment varied among weevil populations and was negatively correlated with the respiration rate and body mass of the insect. Phosphine produced little lysis of mitochondria and the more phosphine‐resistant population exhibited a slightly higher mitochondria fluorescence intensity under confocal imaging. Therefore, reduced respiration rate is correlated with reduced phosphine activity, but its association with high mitochondria fluorescence intensity in muscle cells seems marginal. There was no association between mitochondrial lineages and phosphine susceptibility, which evolved independently, and the mitochondrial gene fragments of cytochrome oxidase I and II were not useful molecular markers of phosphine susceptibility.     

Entamoeba, giardia and toxoplasma: clones or cryptic species?

The availability of molecular markers has renewed interest in the taxonomy of parasitic protozoa at the subspecific and specific levels. Nevertheless, the conclusions reached are heavily dependent upon the way the data are analyzed. Some authors have emphasized the value of genetic distances to propose the creation o f new species, while others have rather favoured a population genetic approach to account for the intraspecific variability of parasites. In this article, using three illustrative cases, Michel Tibayrenc shows that dissimilar taxonomic approaches can be built from quite comparable sets of data.     

Pelvic anti-predator armour reduction in Norwegian populations of the threespine stickleback: a rare phenomenon with adaptive implications?

In order to search for armour reductions in the anti-predator armour apparatus of the threespine stickleback Gasterosteus aculeatus , we studied populations from 200 coastal lakes and 32 marine and estuarine sites in Norway. We scored the presence of reductions in the pelvic apparatus in these populations, measured the length of the second dorsal fin and pelvic spine and counted lateral plates in a subset of 96 populations. Then we looked for the relation between pelvic reduction and number of lateral plates and lengths of the second dorsal spine and pelvic spine. We also observed whether pelvic reduced fish had asymmetric development on the right or the left side of the pelvis. Pelvic reduction was not found in marine and estuarine sticklebacks (with one single exception), but in freshwater it occurred in four out of 200 lakes. The amount of pelvic reduction differed from 5% to 68% in the four populations. There appears to be a correlation between pelvic reduction and spine lengths at the population level, but not plate number. Further, it appears to be difficult to explain the occurrence of pelvic reduction in Norway with the factors proposed to be responsible for pelvic reduction in other regions.     

Malaria parasites: Randomly interbreeding or 'clonal' populations?

The 'clonality' hypothesis proposed by Michel Tibayrenc and his colleagues(1) has stimulated a long-overdue debate on the genetic structure of populations of protozoan parasites. A critical aspect of the hypothesis is the role of a sexual phase in the life cycle of these organisms. In the malaria parasite, Plasmodium, the existence of a sexual phase is unquestioned and is, indeed, a compulsory part of the cycle in the mosquito host. For this parasite, therefore, the principal question to be addressed, here by David Walliker, is whether populations of this parasite in nature are in a state of random mating (panmixia) or whether they comprise a limited number of clones which only occasionally undergo crossmating.     

Nuclear and mitochondrial DNA repair: similar pathways?

Mitochondrial DNA (mtDNA) alterations are implicated in a broad range of human diseases and alterations of the mitochondrial genome are assumed to be a result of its high susceptibility to oxidative damage and its limited DNA repair compared to nuclear DNA (nDNA). Characterization of DNA repair mechanisms has generally focused on these processes in nDNA but increasing interest and research effort have contributed to our knowledge of the mechanisms underlying DNA repair in mitochondria. In this review, we make comparisons between nDNA and mtDNA repair pathways and propose a model for how these pathways interact in mitochondria.     

What regulates mitochondrial DNA copy number in animal cells?

The study of the control of mitochondrial DNA copy number spans several decades and has identified many factors involved in the replication of the mitochondrial genome. However, the mechanisms involved in the regulation of this process are still obscure, particularly in animal cells. During the past decade, however, the identification of human diseases associated with drastically reduced levels of mtDNA caused renewed interest in this topic. Here, I will discuss recent work that sheds some light on how animal cells might maintain and control mtDNA levels.     

Keep your feet warm? A cryptic refugium of trees linked to a geothermal spring in an ocean of glaciers

Up to now, the most widely accepted idea of the periglacial environment is that of treeless ecosystems such as the arctic or the alpine tundra, also called the tabula rasa paradigm. However, several palaeoecological studies have recently challenged this idea, that is, treeless environments in periglacial areas where all organisms would have been exterminated near the glacier formed during the Last Glacial Maximum, notably in the Scandinavian mountains. In the Alps, the issue of glacial refugia of trees remains unanswered. Advances in glacier reconstructions show that ice domes did not cover all upper massifs, but glaciers filled valleys. Here, we used fossils of plant and malacofauna from a travertine formation located in a high mountain region to demonstrate that trees (Pinus, Betula) grew with grasses during the Lateglacial‐Holocene transition, while the glacier fronts were 200–300 m lower. The geothermal travertine started to accumulate more than 14,500 years ago, but became progressively more meteogene about 11,500 years ago due to a change in groundwater circulation. With trees, land snails (gastropods) associated to woody or open habitats and aquatic mollusc were also present at the onset of the current interglacial, namely the Holocene. The geothermal spring, due to warm water and soil, probably favoured woody glacial ecosystems. This new finding of early tree growth, combined with other scattered proofs of the tree presence before 11,000 years ago in the western Alps, changes our view of the tree distribution in periglacial environments, supporting the notion of tree refugia on nunataks in an ocean of glaciers. Therefore, the tabula rasa paradigm must be revisited because it has important consequences on the global changes, including postglacial plant migrations and biogeochemical cycles.     

Viral proteins functioning in organelles: a cryptic origin?

Although mitochondria derive from alpha-proteobacteria, many proteins acting in this organelle did not originate from bacteria. In particular, phylogenetic evidence indicates that RNA polymerase, DNA polymerase and DNA primase--with homologues encoded by T3/T7-like bacteriophages--have replaced the ancestral proteins of bacterial origin. To date, there was no clear explanation for this puzzling observation. Bacterial genomics has now revealed the presence of cryptic prophages that are related to T3/T7 in several genomes of proteobacteria. We propose that such a prophage was present in the ancestral alpha-proteobacterium at the origin of mitochondria and that RNA polymerase, DNA polymerase and DNA primase encoded by this prophage replaced the original bacterial enzymes to function in mitochondria. Another T3/T7 viral-like RNA polymerase is functional in the chloroplast, indicating that a strong selection pressure has favored replacement of some cellular proteins by viral proteins in organelle evolution.     

The mitochondrial theory of aging: dead or alive?

The mitochondrial theory of aging is based around the idea of a vicious cycle, in which somatic mutation of mtDNA engenders respiratory chain dysfunction, enhancing the production of DNA-damaging oxygen radicals. In turn, this is proposed to result in the accumulation of further mtDNA mutations. Finally, a bioenergetic crisis leads to overt tissue dysfunction and degeneration. A substantial body of circumstantial evidence seems to support this idea. However, the extent of detectable mtDNA mutation is far less than can easily be reconciled to this hypothesis, unless it is assumed that a subset of cells with much higher than average mtDNA mutation load is systematically lost by apoptosis. A rigorous test of the hypothesis remains to be undertaken, but would require a direct manipulation of the rate of mtDNA mutagenesis, to test whether this could alter the kinetics of aging.     

Running on empty: Does mitochondrial DNA mutation limit replicative lifespan in yeast?

Mitochondrial DNA (mtDNA) mutations escalate with increasing age in higher organisms. However, it has so far been difficult to experimentally determine whether mtDNA mutation merely correlates with age or directly limits lifespan. A recent study shows that budding yeast can also lose functional mtDNA late in life. Interestingly, independent studies of replicative lifespan (RLS) and of mtDNA-deficient cells show that the same mutations can increase both RLS and the division rate of yeast lacking the mitochondrial genome. These exciting, parallel findings imply a potential causal relationship between mtDNA mutation and replicative senescence. Furthermore, these results suggest more efficient methods for discovering genes that determine lifespan.