Tree of Life

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David Zeigler - One of the best experts on this subject based on the ideXlab platform.

  • Phylogeny—The Tree of Life
    Evolution, 2014
    Co-Authors: David Zeigler
    Abstract:

    One of the most amazing aspects of evolutionary theory is that of common descent—that all Life forms are actually related in a genetic and phylogenetic sense. In short, all Life forms are “cousins” to a greater or lesser extent. This being the case, biologists strive to decipher the exact nature of these relationships such that a Tree of Life can be constructed that will show the evolutionary descent and relationships of all forms of Life on Earth—all lines of descent. Great progress has been made in this regard, and more will certainly occur in the future. Many sources of evidence are used in this work, but comparative genomics has become the prime and ultimate source of information useful in deciphering these relationships.

Pedro Cardoso - One of the best experts on this subject based on the ideXlab platform.

  • Global wildLife trade permeates the Tree of Life
    Biological conservation, 2020
    Co-Authors: Caroline Sayuri Fukushima, Stefano Mammola, Pedro Cardoso
    Abstract:

    Abstract Legal and illegal wildLife trade is a multibillion dollar industry that is driving several species toward extinction. Even though wildLife trade permeates the Tree of Life, most analyses to date focused on the trade of a small selection of charismatic vertebrate species. Given that vertebrate taxa represent only 3% of described species, this is a significant bias that prevents the development of comprehensive conservation strategies. In this short contribution, we discuss the significance of global wildLife trade considering the full diversity of organisms for which data are available in the IUCN database. We emphasize the importance of being fast and effective in filling the knowledge gaps about non-vertebrate Life forms, in order to achieve an in-depth understanding of global trading patterns across the full canopy of the Tree of Life, and not just its most appealing twig.

Guenther Witzany - One of the best experts on this subject based on the ideXlab platform.

  • Viruses are essential agents within the roots and stem of the Tree of Life
    Journal of Theoretical Biology, 2010
    Co-Authors: Luis P. Villarreal, Guenther Witzany
    Abstract:

    In contrast with former definitions of Life limited to membrane-bound cellular Life forms which feed, grow, metabolise and replicate (i) a role of viruses as genetic symbionts, (ii) along with peripheral phenomena such as cryptobiosis and (iii) the horizontal nature of genetic information acquisition and processing broaden our view of the Tree of Life. Some researchers insist on the traditional textbook conviction of what is part of the community of Life. In a recent review they assemble four main arguments which should exclude viruses from the Tree of Life because of their inability to self-sustain and self-replicate, their polyphyly, the cellular origin of their cell-like genes and the volatility of their genomes. In this article we will show that these features are not coherent with current knowledge about viruses but that viral agents play key roles within the roots and stem of the Tree of Life.

  • Viruses are essential agents within the roots and stem of the Tree of Life.
    Journal of Theoretical Biology, 2009
    Co-Authors: Luis P. Villarreal, Guenther Witzany
    Abstract:

    Abstract In contrast with former definitions of Life limited to membrane-bound cellular Life forms which feed, grow, metabolise and replicate (i) a role of viruses as genetic symbionts, (ii) along with peripheral phenomena such as cryptobiosis and (iii) the horizontal nature of genetic information acquisition and processing broaden our view of the Tree of Life. Some researchers insist on the traditional textbook conviction of what is part of the community of Life. In a recent review [Moreira, D., Lopez-Garcia, P., 2009. Ten reasons to exclude viruses from the Tree of Life. Nat. Rev. Microbiol. 7, 306–311.] they assemble four main arguments which should exclude viruses from the Tree of Life because of their inability to self-sustain and self-replicate, their polyphyly, the cellular origin of their cell-like genes and the volatility of their genomes. In this article we will show that these features are not coherent with current knowledge about viruses but that viral agents play key roles within the roots and stem of the Tree of Life.

James A Lake - One of the best experts on this subject based on the ideXlab platform.

  • Genome beginnings: rooting the Tree of Life
    Philosophical transactions of the Royal Society of London. Series B Biological sciences, 2009
    Co-Authors: James A Lake, Craig W Herbold, Ryan G Skophammer, Jacqueline A Servin
    Abstract:

    A rooted Tree of Life provides a framework to answer central questions about the evolution of Life. Here we review progress on rooting the Tree of Life and introduce a new root of Life obtained through the analysis of indels, insertions and deletions, found within paralogous gene sets. Through the analysis of indels in eight paralogous gene sets, the root is localized to the branch between the clade consisting of the Actinobacteria and the double-membrane (Gram-negative) prokaryotes and one consisting of the archaebacteria and the firmicutes. This root provides a new perspective on the habitats of early Life, including the evolution of methanogenesis, membranes and hyperthermophily, and the speciation of major prokaryotic taxa. Our analyses exclude methanogenesis as a primitive metabolism, in contrast to previous findings. They parsimoniously imply that the ether archaebacterial lipids are not primitive and that the cenancestral prokaryotic population consisted of organisms enclosed by a single, ester-linked lipid membrane, covered by a peptidoglycan layer. These results explain the similarities previously noted by others between the lipid synthesis pathways in eubacteria and archaebacteria. The new root also implies that the last common ancestor was not hyperthermophilic, although moderate thermophily cannot be excluded.

  • Evidence for a new root of the Tree of Life.
    Systematic biology, 2008
    Co-Authors: James A Lake, Jacqueline A Servin, Craig W Herbold, Ryan G Skophammer
    Abstract:

    Directed indels, insertions or deletions within paralogous genes, have the potential to root the Tree of Life. Here we apply the top-down rooting algorithm to indels found in PyrD (dihydroorotate dehydrogenase), a key enzyme involved in the de novo biosynthesis of pyrimidines, and HisA (P-ribosylformimino-AICAR-P-isomerase), an essential enzyme in the histidine biosynthesis pathway. Through the comparison of each indel with its two paralogous outgroups, we exclude the root of the Tree of Life from the clade that encompasses the Actinobacteria, the double-membrane prokaryotes, and their last common ancestor. In combination with previous indel rooting studies excluding the root from a clade consisting of the Firmicutes, the Archaea, and their last common ancestor, this provides evidence for a unique eubacterial root for the Tree of Life located between the actinobacterial-double-membrane clade and the archaeal-firmicute clade. Mapping the phylogenetic distributions of genes involved in peptidoglycan and lipid synthesis onto this rooted Tree parsimoniously implies that the cenancestral prokaryotic population consisted of organisms enclosed by a single, ester-linked lipid membrane, covered by a peptidoglycan layer.

  • Decoding the genomic Tree of Life.
    Proceedings of the National Academy of Sciences of the United States of America, 2005
    Co-Authors: Anne B Simonson, Jacqueline A Servin, Ryan G Skophammer, Craig W Herbold, Maria C Rivera, James A Lake
    Abstract:

    Genomes hold within them the record of the evolution of Life on Earth. But genome fusions and horizontal gene transfer (HGT) seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic Tree of Life. HGT among prokaryotes is not random, however. Some genes (informational genes) are more difficult to transfer than others (operational genes). Furthermore, environmental, metabolic, and genetic differences among organisms restrict HGT, so that prokaryotes preferentially share genes with other prokaryotes having properties in common, including genome size, genome G+C composition, carbon utilization, oxygen utilization/sensitivity, and temperature optima, further complicating attempts to reconstruct the Tree of Life. A new method of phylogenetic reconstruction based on gene presence and absence, called conditioned reconstruction, has improved our prospects for reconstructing prokaryotic evolution. It is also able to detect past genome fusions, such as the fusion that appears to have created the first eukaryote. This genome fusion between a deep branching eubacterium, possibly an ancestor of the cyanobacterium and a proteobacterium, with an archaeal eocyte (crenarchaea), appears to be the result of an early symbiosis. Given new tools and new genes from relevant organisms, it should soon be possible to test current and future fusion theories for the origin of eukaryotes and to discover the general outlines of the prokaryotic Tree of Life.

  • Mix and Match in the Tree of Life
    Science (New York N.Y.), 1999
    Co-Authors: James A Lake, Ravi Jain, Maria C Rivera
    Abstract:

    Genes for ribosomal RNA have been used to decipher the evolutionary relationship between eukaryotes and prokaryotes. However, as Lake and colleagues point out in their Perspective, the availability of complete genome sequences for many bacteria (prokaryotes) and for the yeast (a eukaryote) has called into question long-held views about the evolutionary Tree of Life. The Perspective discusses the emerging notion of chimerism in prokaryotic and eukaryotic genomes, which arises through transfer of groups of functionally similar genes between organisms.

Jean-michel Claverie - One of the best experts on this subject based on the ideXlab platform.

  • Editorial: Viruses, Genetic Exchange, and the Tree of Life
    Frontiers in Microbiology, 2019
    Co-Authors: Nikos Kyrpides, Simon Roux, Arshan Nasir, Gustavo Caetano-anollés, Jean-michel Claverie
    Abstract:

    Editorial on the Research Topic Viruses, Genetic Exchange, and the Tree of Life We live in exciting times for microbiology research. The significant technological and scientific advancements in the past decades have now enabled scientists to pursue discovery and description of novel microbial and viral linages from previously uncharted Earth habitats. Two such discoveries are particularly exciting and noteworthy in this regard. First, the discovery of the first "giant virus, " Acanthamoeba polyphaga mimivirus, in 2003, and several others thereafter, posed intriguing questions regarding virus origins, evolution, classification, and their place in the "Tree of Life." Second, the discoveries of "Lokiarchaeota" and several other closely-related archaeal members that encode several eukaryote-specific proteins challenged the three-domain canonical structure of the Tree of Life. These discoveries have reopened debates on central questions in evolutionary biology research such as the origin of viruses, the origin of eukaryotes, evolutionary relationship between Archaea and Eukarya, and the structure and topology of the Tree of Life. In this Research Topic, we received a broad range of contributions addressing these and other related questions. Moelling and Broecker discussed the "virus first" model for the evolution of Life on Earth. They provided several examples of virus diversity and abundance in a range of Earth environments and in the mammalian genomes. According to their view, ribozymes and viroids could have started early evolution albeit they also acknowledged competing alternatives such as the "proteins first" and the "metabolism first" scenarios of origins of Life. In a separate contribution from the same authors,