The universal tree of life: an update
Systematics - field of biology dealing with diversity and evolutionary history of life. Includes Nomenclature. Hierarchical Ranks: Domain. Kingdom. Phylum. Class. Order Cladograms can be “flipped” at nodes, show same relationships. Fig. 2nd: Determine what Kingdom an organism belongs to – write in pencil. At what classification level does the evolutionary relationship between cats and. Classifying things into groups helps us to see relationships and understand the world Carl Woese () 6 kingdoms- Plants, Animals, Eubacteria, Archebacteria, is based on molecular biology and groups all organisms into three domains.
Furthermore, several detailed internal branches within each domain are either controversial, such as the presence of Chlamydiae and Planctomycetes in different bacterial superphyla Kamke et al. This unrooted tree depicts each domain as a radial form with many phyla, without resolving the relationships between phyla within domains.
- The universal tree of life: an update
- Kingdoms & Domains Chapter 18-3
- 5 Kingdom Classification PowerPoint PPT Presentations
However, like all previous trees, this tree does not show some major lineages identified in the past decade, such as the Thaumarchaeota, which are now recognized as one of the three major archaeal phyla Brochier-Armanet et al. Problems with Textbook Trees The universal trees of the s 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 s but is the result of a long branch attraction artifact.The Three Domains of Life
At the beginning of this century, it was acknowledged that all major eukaryotic divisions should be somewhere in the crown Embley and Hirt, ; Keeling and McFadden, ; Philippe and Adoutte, ; Gribaldo and Philippe, Another problem still present in many textbook trees is the position of hyperthermophiles.
All rDNA trees of the s were rooted within hyperthermophilic archaea and bacteria Woese et al. In particular, the hyperthermophilic bacteria of the genera Thermotoga and Aquifex were the two most basal bacterial lineages in all these trees.
However, the analysis of ribosomal RNA sequences at slowly evolving nucleotide positions Brochier and Philippe, and phylogenetic analyses based on protein sequences do not support the deep branching of Thermotoga and Aquifex in the bacterial tree Boussau et al.
The exact position of these hyperthermophilic bacteria currently remains controversial, because of the unusual extent of LGT that occurred between these bacteria and some other bacterial groups Boussau et al.
However, early reports noted that both features could be explained by the very high GC content of the ribosomal RNA of hyperthermophiles that limits the sequence space available for the evolution of these molecules Forterre, ; Galtier et al. Indeed, the reconstruction of ribosomal RNA and protein sequences in LUCA shed serious doubt on its hyperthermophilic nature, and suggests instead that it was either a mesophilic or a moderate thermophilic organism Galtier et al. This result is in agreement with the facts that specific thermoadaptation features of lipids in Archaea and Bacteria are not homologous and that reverse gyrase, a protein required for life at very high temperature, was probably not present in the common ancestor of Archaea and Bacteria Forterre, ; Brochier-Armanet and Forterre, ; Glansdorff et al.
These observations suggest that thermal adaptation from LUCA to the ancestors of Archaea and Bacteria took place from cold to hot and not the other way around. A Tree or a Ring? The most recent version of ring of life scenario is that eukaryogenesis was triggered by the engulfment of an alpha-proteobacterium by a wall-less giant archaeon capable of phagocytosis Martijn and Ettema, Proponents of fusion association scenarios argue that such fusion is required to explain why eukaryotic genomes contain both archaeal and bacterial-like genes.
However, this is not the case, since the presence of archaeal-like genes in Eukarya is a logical consequence of the sisterhood of Archaea and Eukarya, whereas the presence of bacterial-like genes is the expected result of mitochondrial endosymbiosis. Additional bacterial genes might have been introduced in proto-eukaryotes by LGT Doolittle,which may have been partly mediated by large DNA viruses Forterre, a.
These scenarios have been criticized by several authors, as being biologically unsound Woese, ; Kurland et al. In particular, Woese argued that: The universal tree should depict evolutionary relationships between domains defined according to the translation apparatus reflecting the history of cells and their envelope; Woese et al. This is well illustrated by the case of Plantae.
Kingdoms and Domains ppt
The tree of any particular taxonomic unit is indeed not affected by the presence or absence of endosymbionts in some of its branches! This is not the case, because the eukaryotic ribosome is not a mixture of archaeal and bacterial ribosomes; it shares 33 proteins with archaeal ribosomes that are not present in Bacteria, but none with the bacterial ribosome that are not present in Archaea Lecompte et al.
Also, because the number of different possible sequences of ribosomal RNA is so large that the similarity in two sequences always indicates some phylogenetic relationship. However, it is the degree of similarity in ribosomal RNA sequences between two organisms that indicates their relative evolutionary relatedness. The studies of Carl Woese and his colleagues based on comparative sequencing of 16S prokaryotic and 18S eukaryotic ribosomal RNA have resulted in the proposal of a universal phylogenetic tree of life on earth Fig.
Also, the innovative nature of the universal phylogenetic tree became clear as both prokaryotic and eukaryotic species could be analysed together to provide: However, the three phylogenetically distinct lineages or group of cells are called domains and represent the Bacteria, the Archaea, and the Eukarya.
Kingdoms and Domains ppt
The domain Bacteria consists of prokaryotic cells possessing primarily diacyl glycerol diaster lipids in their membranes and bacterial rRNA. The prokaryotic cells having isoprenoid glycerol diether or diglycerol tetra-ether lipids in their membranes and archacal rRNA constitutes the domain Archaea. The domain Eukarya represents the eukaryotic organisms possessing primarily glycerol fatty acyl diaster membrane lipids and eukaryotic rRNA. However, the domains are given rank above the kingdom or phylum levels and differ markedly from one another Table 2.
The domain Bacteria, as said earlier, consists of enormous variety of prokaryotes that possess primarily diacyl glycerol diaster lipids in their membranes and bacterial rRNA. Among Bacteria, many phylogenetic lineages or groups have been discovered; the major lineages or groups of this domain shown in Fig. Several soil and water inhabiting, and parasitic bacteria are the members of Proteobacteria. It also includes lactic acid bacteria e. Streptococcus, Lactobacillus and the mycoplasmas.
The domain Archaea Fig.
Three Domains of Life Protists
Most crenarchaeotes are hyperthermophylic having ability to grow at even or above the boiling point of water e. By contrast with the hyperthermophiles, cold-dwelling crenarchaeotes thrive even in frigid waters such as those of the Antarctic.
Many of them are extreme halophiles i. Methanogenium, an euryarchaeote, has recently been isolated from Ace Lake of Antarctica. However, mixed laboratory cultures of this group of Archaea clearly indicate that they are hyperthermophilic.