The basal branching point in the Coleoptera tree represents the ancestor of all beetles. This ancestor diversified over time into several descendent subgroups, which are represented as internal nodes branching points and terminal taxa at the tips of the beetle tree.
Beginning at the root on the left, the diagram shows that the ancestral beetle lineage gave rise, on the one hand, to members of the extinct Paleozoic group Protocoleoptera, and on the other to the ancestor of the remaining beetles. This ancestor in turn split into a species that gave rise to the extinct family Permocupedidae, and another that gave rise to the remainder of the beetles. Further splitting of ancestral species would lead us to the terminal taxa in the diagram, where we see Polyphaga and Myxophaga on adjacent branches.
The ancestral species of these two groups split in two to give rise to one species that was the ancestor of the Polyphaga, and another species that was the ancestor of the Myxophaga. Even though it isn't shown on this diagram, the splits implied in this tree probably happened in the Permian period, before the time of the dinosaurs. Terminal taxon names that are underlined and printed in blue represent links to ToL pages about a particular subgroup.
By clicking on the names of these groups, ToL visitors can thus move up to a branch higher in the tree of life. For example, in the beetle tree, one can move up to the branch pages of the beetle subgroups Polyphaga, Myxophaga, Adephaga, and Archostemata.
On each of these pages, there will then be another tree diagram with links to subgroups leading further up the branches of the tree of life. In this way, one can move from Coleoptera to Adephaga to Carabidae and then to Gehringia olympica , which is a beetle species, representing a leaf on the tree of life.
Terminal taxon links in ToL tree diagrams let visitors move up the branches of the tree of life, all the way to leaf pages. The root of the beetle tree connects the beetles to their containing group, the Endopterygota insects with complete metamorphosis.
When the king realized that she was a goddess, he told her she could have anything in his kingdom. Naturally, Isis asked for the pillar, which the king graciously gave to her. Isis returned the pillar to Egypt and planted it in the ground. Now, there is more to this story and what happened to Osiris.
However, as the story goes, the tree that had been turned into a pillar and then became a tree again is the basis for the Egyptian Tree of Life. Other Egyptian myths claim that all of the gods were all born from acacia trees. However, as Osiris became the god of agriculture, the underworld, and rebirth, the Egyptian Tree of Life is representative of the cycle of life, the connection between the underworld, the physical world, and the gods. In Africa, the closest association with a Tree of Life is the baobab tree.
Creation stories throughout the continent attest that it was God who created the baobab tree. In fact, these massive trees pre-date human beings, so as long as people have lived in Africa, there have been baobab trees. Explanations for why the baobab tree looks the way it does center around God changing his mind and turning the tree upside down and then re-planting it in the Earth. Some African tribes believed that baobab trees had mystical properties. For example, picking the white flowers from the tree would invite a lion to eat you.
Or, if you soaked baobab seeds in water and then drank the water, crocodiles would not attack you. Likewise, soaking a baby in water that contained baobab bark would make the baby strong like the baobab tree.
Greek mythology has a few different stories about magical trees, which closely resemble the idea of the Tree of Life or the World Tree. In one story, Zeus marries the goddess of the Earth, Gaia , and from their union a giant oak tree sprouts. In other versions, as in the story of Osiris, Zeus becomes part of the tree.
And its branches could reach the stars. At first Hera appointed some nymphs to tend to the tree. So, Hera got a dragon named Ladon to guard the tree. In the Bible, the Tree of Knowledge is similar to the World Tree and Tree of Life in other cultures in that it is a source of universal wisdom.
In some creation stories, the Tree of Knowledge is one of two mystical trees, while in others, the trees are one in the same. What is clear in the Book of Genesis is that Adam and Eve were not supposed to eat the fruit from the Tree of Knowledge. While in Nordic mythology, Odin had to prove that he was worthy of accessing that kind of knowledge, in the Bible, Adam and Eve were deemed unworthy at the start. However, later in the Bible, in the Book of Revelation, human beings are shown how they can safely access the wisdom of Tree of Knowledge, which is then referred to as the Tree of Life.
A Tree of Life also appears in the Quran. Referred to as Tree of Immortality, the tree also grows in the Garden of Eden. Because they make the mistake of eating from the tree, Allah sends Adam and Even to Earth, where they must live and learn to repent from their mistakes. However, Allah assures them that while on Earth they will have guidance.
Kabbalah is an ancient form of Jewish mysticism whose followers say dates back to when the Universe was first created. In written history, Kabbalah came to the forefront in the 12th and 13th centuries in southern Spain and France. Essentially, as is the case with mysticism in other religious faiths, followers of Kabbalah believe that we all have a direct union with God, or the source of creation. In Kabbalah, the Tree of Life is depicted as a symbol that contains 10 Sefirot, or channels of divine energy and spiritual practice.
The place on the branch where the trait appears indicates the evolutionary root of that trait. No animal before that time has this trait; every animal on the branch after does. All the animals to the left of the lamprey, including the lamprey have a braincase and backbone. And none of the organisms to the right do. This is one of a relatively small number of three-domain trees constructed from molecular information so far, and the first comprehensive tree to be published since the development of genome-resolved metagenomics.
We highlight all major lineages with genomic representation, most of which are phylum-level branches see Supplementary Fig. However, we separately identify the Classes of the Proteobacteria, because the phylum is not monophyletic for example, the Deltaproteobacteria branch away from the other Proteobacteria, as previously reported 2 , The tree includes 92 named bacterial phyla, 26 archaeal phyla and all five of the Eukaryotic supergroups.
Major lineages are assigned arbitrary colours and named, with well-characterized lineage names, in italics. Lineages lacking an isolated representative are highlighted with non-italicized names and red dots.
For details on taxon sampling and tree inference, see Methods. The names Tenericutes and Thermodesulfobacteria are bracketed to indicate that these lineages branch within the Firmicutes and the Deltaproteobacteria, respectively. Eukaryotic supergroups are noted, but not otherwise delineated due to the low resolution of these lineages.
The CPR phyla are assigned a single colour as they are composed entirely of organisms without isolated representatives, and are still in the process of definition at lower taxonomic levels. The complete ribosomal protein tree is available in rectangular format with full bootstrap values as Supplementary Fig. The tree in Fig. The lower support for deep branch placements is a consequence of our prioritization of taxon sampling over number of genes used for tree construction.
As proposed recently, the Eukarya, a group that includes protists, fungi, plants and animals, branches within the Archaea, specifically within the TACK superphylum 21 and sibling to the Lokiarchaeota The two-domain Eocyte tree and the three-domain tree are competing hypotheses for the origin of Eukarya 5 ; further analyses to resolve these and other deep relationships will be strengthened with the availability of genomes for a greater diversity of organisms.
Important advantages of the ribosomal protein tree compared with the SSU rRNA gene tree are that it includes organisms with incomplete or unavailable SSU rRNA gene sequences and more strongly resolves the deeper radiations. Ribosomal proteins have been shown to contain compositional biases across the three domains, driven by thermophilic, mesophilic and halophilic lifestyles as well as by a primitive genetic code Continued expansion of the number of genome sequences for non-extremophile Archaea, such as the DPANN lineages 8 , 13 , may allow clarification of these compositional biases.
A striking feature of this tree is the large number of major lineages without isolated representatives red dots in Fig. Many of these lineages are clustered together into discrete regions of the tree. Based on information available from hundreds of genomes from genome-resolved metagenomics and single-cell genomics methods to date, all members have relatively small genomes and most have somewhat if not highly restricted metabolic capacities 7 , 13 , Many are inferred and some have been shown to be symbionts 7 , 25 , Thus far, all cells lack complete citric acid cycles and respiratory chains and most have limited or no ability to synthesize nucleotides and amino acids.
It remains unclear whether these reduced metabolisms are a consequence of superphylum-wide loss of capacities or if these are inherited characteristics that hint at an early metabolic platform for life. If inherited, then adoption of symbiotic lifestyles may have been a later innovation by these organisms once more complex organisms appeared.
Figure 2 presents another perspective, where the major lineages of the tree are defined using evolutionary distance, so that the main groups become apparent without bias arising from historical naming conventions. This depiction uses the same inferred tree as in Fig. We chose an average branch length that best recapitulated the current taxonomy smaller values fragmented many currently accepted phyla and larger values collapsed accepted phyla into very few lineages, see Methods.
Evident in Fig. The CPR is early-emerging on the ribosomal protein tree Fig. Regardless of branching order, the CPR, in combination with other lineages that lack isolated representatives red dots in Fig. Notably, some well-accepted phyla become single groups and others are split into multiple distinct groups. We undertook this analysis to provide perspective on the structure of the tree, and do not propose the resulting groups to have special taxonomic status. The massive scale of diversity in the CPR and the large fraction of major lineages that lack isolated representatives red dots are apparent from this analysis.
Domain Bacteria includes more major lineages of organisms than the other Domains. We do not attribute the smaller scope of the Archaea relative to Bacteria to sampling bias because metagenomics and single-cell genomics methods detect members of both domains equally well. Consistent with this view, Archaea are less prominent and less diverse in many ecosystems for example, seawater 27 , hydrothermal vents 28 , the terrestrial subsurface 15 and human-associated microbiomes The lower apparent phylogenetic diversity of Eukarya is fully expected, based on their comparatively recent evolution.
The tree of life as we know it has dramatically expanded due to new genomic sampling of previously enigmatic or unknown microbial lineages. This depiction of the tree captures the current genomic sampling of life, illustrating the progress that has been made in the last two decades following the first published genome.
What emerges from analysis of this tree is the depth of evolutionary history that is contained within the Bacteria, in part due to the CPR, which appears to subdivide the domain. Most importantly, the analysis highlights the large fraction of diversity that is currently only accessible via cultivation-independent genome-resolved approaches.
A data set comprehensively covering the three domains of life was generated using publicly available genomes from the Joint Genome Institute's IMG-M database img. From IMG-M, genomes were sampled such that a single representative for each defined genus was selected. For phyla and candidate phyla lacking full taxonomic definition, every member of the phylum was initially included.
Subsequently, these radiations were sampled to an approximate genus level of divergence based on comparison with taxonomically described phyla, thus removing strain- and species-level overlaps. Finally, initial tree reconstructions identified aberrant long-branch attraction effects placing the Microsporidia, a group of parasitic fungi, with the Korarchaeota.
The Microsporidia are known to contribute long branch attraction artefacts confounding placement of the Eukarya 33 , and were subsequently removed from the analysis. This study includes 1, organisms from lineages for which genomes were not previously available.
The organisms were present in samples collected from a shallow aquifer system, a deep subsurface research site in Japan, a salt crust in the Atacama Desert, grassland meadow soil in northern California, a CO 2 -rich geyser system, and two dolphin mouths.
Genomes were reconstructed from metagenomes as described previously 7. Genomes were additionally required to have consistent nucleotide composition and coverage across scaffolds, as determined using the ggkbase binning software ggkbase.
This contributed marker gene information for 1, newly sampled organisms, whose genomes were reconstructed for metabolic analyses to be published separately. The concatenated ribosomal protein alignment was constructed as described previously The 16 alignments were concatenated, forming a final alignment comprising 3, genomes and 2, amino-acid positions.
A maximum likelihood tree was constructed using RAxML v. A total of bootstrap replicates were conducted under the rapid bootstrapping algorithm, with sampled to generate proportional support values. To construct Fig.
Average branch length calculations were implemented in the Interactive Tree of Life online interface 37 using the formula:. We tested values between 0. As genome sampling was confined to the genus level, we do not anticipate this selection process will have any impact on the resultant tree. The RAxML inference included the calculation of bootstrap iterations extended majority rules-based bootstopping criterion , with randomly sampled to determine support values.
In both cases, the topology of the tree with the best likelihood was not changed significantly. The alignments and inferred trees under the more stringent gap stripping are available upon request. We have included names for two lineages for which we have previously published complete genomes At the time of submission of the paper describing these genomes 40 , the reviewer community was not uniformly open to naming lineages of uncultivated organisms based on such information.
Given that this practice is now widely used, we re-propose the names for these phyla. The concatenated ribosomal protein and SSU rRNA alignments used for tree reconstruction are included as separate files in the Supplementary Information.
Woese, C. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
Natl Acad. USA 87, — Article Google Scholar. Yarza, P. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nature Rev.
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