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19 Fun Facts Tree Of Life Starting With Ba | Tree Of Life Biology
- These past 20 years, the rooting problem has been neglected—with a few exceptions (see for instance Harish et al., 2013) that I have no space to discuss here. Indeed, “ring of life” scenarios or those in which Eukaryotes originated from Archaea automatically root the tree between Archaea and Bacteria (rejuvenating the pre-Woesien prokaryote/eukaryote paradigm). However, comparative molecular biology has now revealed several situations that can help us to root the universal tree and decide between alternative scenarios. - Source: Internet
- Moreira and colleagues argue that eukaryotic proteins cannot be used to root the archaeal tree if Eukarya emerged from within Archaea. However, in the framework of the classical Woese tree, it makes more sense to root the archaeal tree using eukaryotic proteins as outgroup, because these proteins are much more closely related than bacterial proteins to their archaeal orthologs. Notably, the rooting between Lokiarchaeota/Thaumarchaeota and other Archaea, obtained in that case is more parsimonious than the rooting between Euryarchaeota and other Archaea in explaining the presence in Lokiarchaeota/Thaumarchaeota (including “Aigarchaeota,” see below) of many eukaryotic features lacking in other Archaea (Brochier-Armanet et al., 2008b; Spang et al., 2010, 2015; Koonin and Yutin, 2014). - Source: Internet
- This section on archaeal phylogeny has illustrated the fact that, in addition to the root of the tree itself, several nodes in the archaeal tree are still controversial and require more data and more work to be carried out. These nodes have been marked by circles in blue in the tree of Figure 6. Future progress will probably come from the sequencing of more genomes, especially in poorly represented groups and in the many groups that are presently only known from environmental rDNA sequences. - Source: Internet
- In the tree of Figure 3, I use the terms “synkaryote” and “akaryote” (with and without a nucleus, respectively) instead of eukaryotes and prokaryotes (Forterre, 1992; Harish et al., 2013; Penny et al., 2014). This is because the latter terms are the hallmark of the traditional (pre-Woesian) view of the evolution of life from primitive bacteria (“pro” karyotypes) to lower and finally higher eukaryotes (Forterre, 1992; Pace, 2006; Penny et al., 2014). - Source: Internet
- Importantly, rooting of the universal tree in the “bacterial branch” formally requires giving a name to the clade grouping Archaea and Eukarya. Woese (2000) never proposed such a name, adopting a “gradist” view of life evolution, with the three Domains emerging independently from a “communal LUCA” before the “Darwinian threshold” (Woese, 2000, 2002). In such view, the notion of clade itself cannot be used to group organisms that diverged at the time of LUCA when no real speciation occurred. I have criticized the Darwinian threshold concept, assuming—with many others—that Darwinian evolution started as soon as biological evolution take off (see Forterre, 2012, and references therein). In particular, extensive genes exchanges that possibly take place at the time of LUCA (but see Poole, 2009) cannot be opposed to Darwinian evolution occurring through variation and selection, since gene transfer only corresponds to a specific type of variation (Forterre, 2012). - Source: Internet
- Figure 4. Schematic simplified universal tree updated from Woese et al. (1990). Abbreviations are the same as in Figure 3. - Source: Internet
- I thank Mechthild Pohlschroeder and Sonja-Verena Albers for inviting me to draw an updated version of the universal tree of life and David Prangishvili for suggesting the name Arkarya. I am grateful to Sukhvinder Gill for English corrections and a referee for extensive critical analysis. I am supported by an ERC grant from the European Union’s Seventh Framework Program (FP/2007-2013)/Project EVOMOBIL—ERC Grant Agreement no.340440. - Source: Internet
- Euryarchaeota are divided in two sub-phyla I and II, according to the presence/absence of DNA gyrase, a bacterial DNA topoisomerase that was transferred once in the phylum Euryarchaeota (Raymann et al., 2014). The sub-phylum I Euryarchaeota corresponds to those lacking DNA gyrase and encompasses Thermococcales, Nanoarchaeum, and class I methanogens, whereas sub-phylum I corresponds to those containing DNA gyrase and encompasses Archaeoglobales, Thermoplasmatales, Halobacteriales, and class II methanogens (Forterre et al., 2014b). - Source: Internet
- Another explanation for the existence of non-homologous systems between Archaeal/Eukaryal and Bacteria is that LUCA contained two redundant systems and that one of them was later on lost at random in each domain (Edgell and Doolittle, 1997; Glansdorff et al., 2008). However, it is unlikely that both versions of all non-homologous systems between Archaeal/Eukaryal and Bacteria were present in LUCA. For instance, no modern cells have two non-homologous versions of DNA replication machineries or two versions of RNA polymerases (the bacterial and the archaeal ones). Some systems could have been randomly distributed between LUCA and other contemporary cellular (or viral) lineages, and redistributed thereafter by LGT, but this seems very unlikely in the case of the ribosome. - Source: Internet
- The universal tree published by Gribaldo and co-workers reflects our best present knowledge of the internal branching order within Archaea and recovers the monophyly of most phyla in the three domains (Raymann et al., 2015). Notably, Archaea are rooted in this tree within Euryarchaeota when bacterial proteins are used as an outgroup, suggesting a new root for Archaea. However, Moreira and colleagues found instead that the root of the archaeal tree is located between Euryarchaeota and Crenarchaeota when using a bacterial outgroup (Petitjean et al., 2014). - Source: Internet
- I divide the phylum Euryarchaeota in sub-phylum I (I) and sub-phylum II (II), according to the presence/absence of DNA gyrase (see below; Forterre et al., 2014b). Dotted lines indicate the endosymbiosis events that had a major impact on the history of life by triggering the emergence of both modern eukaryotes (mitochondria) and Plantae (chloroplasts). In particular, this reminds us that the first mitochondriate eukaryote (FME) emerged after the diversification of alpha proteobacteria, indicating that “modern eukarya” are indeed much more recent than Archaea and Bacteria. - Source: Internet
- “Just one example to give you is from seniors. Multiple seniors have told us that they’re skipping doctor’s appointments, they’re not filling prescriptions, which is really concerning,” says Chris West , director of community connections and collaborative learning at the Greater Pittsburgh Community Food Bank. “They’re doing that because they’re trying to make ends meet and get the things they need to get. So that’s where the food bank comes in, to make sure that folks can have food and have money left in their pocket to buy the things they need to buy.” - Source: Internet
- “Out of the ground the LORD God made grow every tree that was delightful to look at and good for food, with the tree of life in the middle of the garden and the tree of the knowledge of good and evil.” Genesis 2: 9 - https://bible.usccb.org/bible/genesis/2 - Source: Internet
- In contrast to class I, the four orders of class II methanogens that are included within neo-euryarchaeota are always paraphyletic in phylogenetic analyses. Methanogens of the recently described order Methanomassiliicoccus form a monophyletic assemblage with Thermoplasmatales, the moderate thermoacidophilic strain Aciduliprofundum boonei and several lineages of uncultivated archaea in a ribosomal protein tree (Borrel et al., 2013). The name Diafoarchaea has been proposed for this major subgroup (superclass) of neo-Euryarchaeota (Petitjean et al., 2015). - Source: Internet
- The rooting of the universal tree in the so-called “bacterial branch” (Figures 3–5) has been often interpreted as suggesting a “prokaryotic phenotype” for LUCA. This is a misleading interpretation that again confuses the phenotypes at the tip and base of a branch. The rooting between a lineage leading to Bacteria and a lineage leading to Archaea and Eukarya is compatible with diverse types of LUCA, including a LUCA with some “eukaryotic-like features” that were lost in Archaea and Bacteria (Forterre, 2013a). - Source: Internet
- The universal trees of the 1990s based on rDNA that are still widely used in textbooks, reviews and seminars provide a misleading view of the history of organisms. For instance, they all depict the division of Eukarya between a crown including Plants, Metazoa, Fungi, and several lineages of protists, and several basal long branches leading to various other unicellular eukaryotes, of which the most basal are protists lacking mitochondria (formerly called Archaezoa). This topology of the eukaryotic tree was very popular in the 1990s but is the result of a long branch attraction artifact. At the beginning of this century, it was acknowledged that all major eukaryotic divisions should be somewhere in the crown (Embley and Hirt, 1998; Keeling and McFadden, 1998; Philippe and Adoutte, 1998; Gribaldo and Philippe, 2002). - Source: Internet
- It is traditionally suggested that the process that led to this transformation was triggered by the endosymbiosis event that created mitochondria (Lane and Martin, 2010). This seems to be a leap of faith, because there is no example of such a drastic transformation of the host molecular fabric at the more basic and fundamental levels (translation, transcription, replication) triggered by an endosymbiotic event (Forterre, 2013a). For instance, Plantae remain bona fide Eukarya (with typical eukaryotic version of all universal proteins) despite the fact that about 20% of their genes originated from cyanobacteria (Martin et al., 2002). - Source: Internet
- Altiarchaeales correspond to a recently described mesophilic archaeum, Candidatus Altiarchaeum hamiconexum, characterized by fascinating appendages (Hami) that groups with Methanococcales in a ribosomal protein tree, but between Euryarchaeota of sub-phyla I and II in a tree based on several other universal proteins (Probst et al., 2014). Since Candidatus A. hamiconexum contain the two DNA gyrase genes, it is located at the base of the neo-euryarchaeota in the tree of Figure 6. - Source: Internet
- As is the case for archaeal/eukaryal relationships, there is probably no valid phylogenetic signal left in the universal protein data set to resolve the rooting of the universal tree by molecular phylogeny. This was confirmed in the case of the elongation factors data set by a cladistic analysis of individual amino-acid alignments that discriminate between primitive and share derived characters (Forterre et al., 1992). Only 23 positions could be subjected to this analysis in the elongation factor data set, of which 22 gave ambiguous results and only one supported bacterial rooting! - Source: Internet
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