Formalizing reliability in the taxonomic congruence approach

In the 'total evidence' approach to phylogenetics, the reliability of a clade is implicitly measured by its degree of support, often embodied in a robustness index such as a bootstrap proportion. In the taxonomic congruence approach, the measurement of reliability has been implemented by various consensus or supertree methods, but was seldom explicitly discussed as such. We explore a reliability index for clades using their repetition across independent data sets. All possible combinations of the elementary data sets are used to compose the sets of independent data sets, across which the repetitions are counted. The more a clade occurs across such independent combinations, the higher its index. However, if other repeated clades occur that are incompatible with that clade, its index is decreased to take into account the uncertainty resulting from conflicting hypotheses. Results can be summarized through a greedy consensus tree in which clades appear according to their repetition indices. This index is tested on a 73 acanthomorph taxa data set composed of five independent molecular markers and multiple combinations of them. On this particular application, we confirm that reliability as defined here and robustness (estimated by bootstrap proportions obtained from a 'total evidence' approach) should be clearly distinguished.     

Defective endoplasmic reticulum-mitochondria contacts and bioenergetics in SEPN1-related myopathy

SEPN1-related myopathy (SEPN1-RM) is a muscle disorder due to mutations of the SEPN1 gene, which is characterized by muscle weakness and fatigue leading to scoliosis and life-threatening respiratory failure. Core lesions, focal areas of mitochondria depletion in skeletal muscle fibers, are the most common histopathological lesion. SEPN1-RM underlying mechanisms and the precise role of SEPN1 in muscle remained incompletely understood, hindering the development of biomarkers and therapies for this untreatable disease. To investigate the pathophysiological pathways in SEPN1-RM, we performed metabolic studies, calcium and ATP measurements, super-resolution and electron microscopy on in vivo and in vitro models of SEPN1 deficiency as well as muscle biopsies from SEPN1-RM patients. Mouse models of SEPN1 deficiency showed marked alterations in mitochondrial physiology and energy metabolism, suggesting that SEPN1 controls mitochondrial bioenergetics. Moreover, we found that SEPN1 was enriched at the mitochondria-associated membranes (MAM), and was needed for calcium transients between ER and mitochondria, as well as for the integrity of ER-mitochondria contacts. Consistently, loss of SEPN1 in patients was associated with alterations in body composition which correlated with the severity of muscle weakness, and with impaired ER-mitochondria contacts and low ATP levels. Our results indicate a role of SEPN1 as a novel MAM protein involved in mitochondrial bioenergetics. They also identify a systemic bioenergetic component in SEPN1-RM and establish mitochondria as a novel therapeutic target. This role of SEPN1 contributes to explain the fatigue and core lesions in skeletal muscle as well as the body composition abnormalities identified as part of the SEPN1-RM phenotype. Finally, these results point out to an unrecognized interplay between mitochondrial bioenergetics and ER homeostasis in skeletal muscle. They could therefore pave the way to the identification of biomarkers and therapeutic drugs for SEPN1-RM and for other disorders in which muscle ER-mitochondria cross-talk are impaired.Subject terms: Chaperones, Respiratory tract diseases     

Patterns of septal biomineralization in Scleractinia compared with their 28S rRNA phylogeny: a dual approach for a new taxonomic framework

A molecular phylogeny of the Scleractinia is reconstructed from approximately 700 nucleotides of the 5'end of the 28S rDNA obtained from 40 species. A comparison of molecular phylogenic trees with biomineralization patterns of coral septa suggests that at least five clades are corroborated by both types of data. Agaricidae and Dendrophylliidae are found to be monophyletic, that is supported by microstructural data. Conversely, Faviidae and Caryophylliidae are found to be paraphyletic: Cladocora should be excluded from the faviids, whereas Eusmilia should be excluded from the caryophylliids. The conclusion is also supported by the positions, sizes and shapes of centres of calcification. The traditional Guyniidae are diphyletic, corroborating Stolarski's hypothesis 'A'. Some results from our most parsimonious trees are not strongly statistically supported but corroborated by other molecular studies and microstructural observations. For example, in the scleractinian phylogenetic tree, there are several lines of evidence (including those from our data) to distinguish a Faviidae–Mussidae lineage and a Dendrophylliidae–Agaricidae–Poritidae–Siderastreidae lineage. From a methodological standpoint, our results suggest that co-ordinated studies creating links between biomineralization patterns and molecular phylogeny may provide an efficient working approach for a re-examination of scleractinian classification. This goal is important because in the evolutionary scheme proposed by Wells that presently remains the basic framework in coral studies, patterns of septal microstructures are involved. Validating from molecular phylogenies a given microstructural character state as a potential synapomorphy for a clade is the only way to include fossils in the coral classification, an approach that should allow the unity of coral classification to be maintained up to the origin of the phylum in the Triassic times.     

La biodiversité : au pays des aveugles le borgne est roi

Our media and policies for environment protection and sustainable development see “Biodiversity” only through what species do (their ecological roles, the “services” they can perform) and forget what species have. However the value we confer to a species cannot be ecologically based only. Rare organs, rare structures, rare character mosaics are valuable as unique products of a historical process even if the species exhibiting them are negligible in terms of ecosystem dynamics. Coelacanths, the platypus, can perfectly disappear from the surface of the planet without any significant ecological impact. The “ecological order” does not reflect the historical order. Systematics is the science of classification whose role is to exhibit this historical order in distribution of attributes among species through phylogenies, and then through classifications. Systematics is forgotten in almost all documents written by scientists to advice politicians on the best way to save biodiversity. Without systematics, we lose the historical dimension of what exists, and we simply lose the knowledge of what is what we are facing.