The expanding Asgard archaea and their elusive relationships with Eukarya

Abstract

The discovery of Asgard archaea and the exploration of their diversity over the last 6 years have deeply impacted the scientific community working on eukaryogenesis, rejuvenating an intense debate on the topology of the universal tree of life (uTol). Here, we discuss how this debate is impacted by two recent publications that expand the number of Asgard lineages and eukaryotic signature proteins (ESPs). We discuss some of the main difficulties that can impair the phylogenetic reconstructions of the uTol and suggest that the debate about its topology is not settled. We notably hypothesize the existence of horizontal gene transfers between ancestral Asgards and proto‐eukaryotes that could result in the observed abnormal behaviors of some Asgard ESPs and universal marker proteins. This hypothesis is relevant regardless of the scenario considered regarding eukaryogenesis. It implies that the Asgards were already diversified before the last eukaryotic common ancestor and shared the same biotopes with proto‐eukaryotes. We suggest that some Asgards might be still living in symbiosis today with modern Eukarya.

Carl Woese: Still ahead of our time

“…The marker selection process is a critical step in phylogenetic analysis since a single misleading protein can completely change the result obtained by the concatenation of dozens of proteins. This has been shown, for instance, in the case of elongation factor EF2 of two lineages (out of 18) of Asgard archaea that did not branch with other Asgard EF2 but as a sister group of eukaryotes, probably because of ancient LGT between these Asgard and proto‐eukaryotes 22,54 . Removal of this protein from the original data set of 36 markers dramatically changed the topology of the final tree, producing a 3D tree in the absence of fast‐evolving species 22 .…”

“…In fact, the classical Woese's tree is most likely still the correct one (Figure 1E). The 2D trees obtained during the last decade can be explained by the presence of fast‐evolving species and small proteins in data sets, combined with the difficulty in recovering the short branch testifying to the monophyly of Archaea (for reviews and recent results, see Ref 54 …”

Sub Magnetic Environmental Biology based on Data Mining Algorithm

“…The magnetic field may directly affect chromate or grid protein, affect the function of grid cells, and then affect the secretion of norepinephrine. It is speculated that chromaffin cells may be an important magnetic response cell, and the magnetic field affects the basic metabolic level of organisms by interfering with the secretion of norepinephrine and epinephrine [18].…”

Les virus et l’émergence des cellules eucaryotes modernes

“…Dans le scénario évolutif dit « deux domaines », selon lequel les eucaryotes seraient issus de l'association entre une archée, appelée Asgard, et une alpha-protéobactérie, il a été proposé que l'ensemble des eucaryovirus seraient les descendants des virus ayant infecté ces deux procaryotes [8] (Figure 2B). Dans l'autre scénario majeur, dit « trois domaines », selon lequel les eucaryotes et les archées partagent un ancêtre commun [9], certains groupes de virus spécifiques des eucaryotes auraient pu émerger avant cet ancêtre, voire avant LUCA 3 , et être ensuite perdus dans les autres domaines (Figure 2C, cercle orange). Ceci pourrait être en particulier le cas des familles de virus à ARN inconnus chez les bactéries, ce qui permet d'imaginer un lien de parenté direct entre les premiers virus à ARN apparus au cours de l'évolution et les virus à ARN des eucaryotes modernes.…”

“…Les deux schémas du haut (A)représentent les relations évolutives entre les eucaryovirus, les bacteriovirus et les archéovirus des deux sphères de virus cosmopolites, les Varidnaviria[6,7] et les Duplodnaviria, montrant que les eucaryovirus se regroupent à part des deux autres ensembles de virus. Au contraire, les eucaryotes se regroupent avec les archées dans l'arbre universel du vivant fondé sur les ARN ribosomiques et/ ou les protéines universelles[9]. Les deux schémas du bas (B, C) représentent les deux scénarios pour l'origine des eucaryotes et de leurs virus.…”