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'The All-Species Living Tree' Project

From Wikipedia, the free encyclopedia

'The All-Species Living Tree' Project logo
'The All-Species Living Tree' Project logo

'The All-Species Living Tree' Project is a collaboration between various academic groups/institutes, such as ARB, SILVA rRNA database project, and LPSN, with the aim of assembling a database of 16S rRNA sequences of all validly published species of Bacteria and Archaea.[1] At one stage, 23S sequences were also collected,[2] but this has since stopped.[3]

Currently there are over 10,950 species in the aligned dataset and several more are being added either as new species are discovered or species that are not represented in the database are sequenced. Initially the latter group consisted of 7% of species.

YouTube Encyclopedic

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Transcription

Taxonomy! It's the science of classifying living things. That sounds exciting. Today we'll basically be learning the Dewey Decimel System of evolution! It's like filing! You must be on the edge of your seat. OK, shut up. When it comes down to it, this science doesn't just categorize organisms, when you look a little deeper, you realize it's telling the story of all life on earth. And it's a pretty good story. Every living thing on this planet is related to every other living thing. If you go far enough back, we all have a common ancestor. An organism that both you and I are descended from. Or something that a star fish and a blue whale are descended from. Or, even weirder, that an oak tree and a salmon are both descended from. That organism lived. It lived very long ago. But it was here. And I dig that. The trick of taxonomy, is basically figuring out where all those branches of the evolutionary tree are, and finding some convenient labels to help us understand all of these remarkable interrelationships. Let's be clear though, taxonomy isn't about describing life in all of it's ridiculous detail, it's mostly about helping humans understand it, because it's way too complicated without structure. To get that structure biologists use the taxonomic system to classify all the organisms on the Earth. It's sometimes called the Phylogenetic Tree, or the Tree of Life, and it illustrates the evolutionary relationships between all living species. There are about 2 million known species, but there could be anywhere from 5 million to 100 million species scientists really have no freaking idea. New species keep getting discovered all the time, and the more organisms we have to keep track of, the more complex the Phylogenetic Tree becomes. So, there's not always a consensus about how to classify this stuff. There's a lot of gray area in the Natural World. Actually, let me rephrase that: the Natural World is one giant Gray Area. Sometimes it's just hard to know where to put a certain group of organisms, and eventually the group gets so big, the classification system has to be messed with to make room for it. So, the system isn't perfect, but it's good enough that we've been using it for around 250 years. [Sniffing] What's that? Do you smell a Bio-lography coming on? Carl Linnaeus was a Swede born in 1707. And early in his career as a botanist he realized that the botanical nomenclature of 18th century Europe was.. well, just crap. For instance, in his day, the "formal" name of a tomato plant was Solanum caule inerme herbaceo, foliis pinnatis incisis, racemis simplicibus. Linnaeus actually said once, "I shudder at the sight of most botanical names given by modern authorities." Not only did this sloppiness bother him, he saw a whole sugarstorm blowing in: New plants were still being discovered in Europe, but that was nothing compared to the crazy stuff that was coming from the New World. Linnaeus saw that pretty soon, naming conventions were just going to collapse under all these new things to name. And THEN what? Linnaeus famously started off by naming himself. He came from a peasant family, and at the time, surnames were just for rich people, so when Carl went to college, they asked him for his surname and he just made one up: Linneaus, after the Linden trees that grew on his family's homestead. Linnaeus got a medical degree and became a professor at Uppsala University where he devoted himself to the study of nomenclature. He had his students go places and bring back specimens for him to study and categorize. The method he eventually adopted was based on morphology, or physical form and structure. This wasn't necessarily a new idea. Back then, people grouped organisms by analogous or homoplasic traits, structures that appear similar but actually come from completely independent origins. By this definition, birds would be more closely related to butterflies than to reptiles because birds and butterflies can both fly. But Linnaeus had a good mind for this stuff and turned out to have a real knack for choosing actual homologous traits for his classification system traits that stem from a common evolutionary ancestor. Linnaeus didn't know jack about evolution Darwin wouldn't come around for another 100 plus years but he just intuited that some traits were more important than others. For instance, he was struck by the fact that reproductive apparatus seemed to be a good way of classifying plants. He also caused a scandal by classifying the Class Mammalia based on the female's ability to produce milk from their nipples. Because apparently that was pretty racy stuff back then. In his lifetime Linnaeus catalogued roughly 7,700 plants and 4,400 animals, and he published his classifications in a catalog called Systema Naturae, which by the time he wrote the 12th edition, was 2,300 pages long. In the meantime, Linneaus actually adopted a personal motto: "God created, Linnaeus organized." Although taxonomy has come a long way since Linnaeus, we still use a bunch of the conventions that he invented. For instance, we still arrange things into taxa, or groups of organisms, and we still us the same Taxa as Linnaeus: kingdom, phylum, class, order, family, genus and species. We also still use Linnaeus' convention of binomial nomenclature using a unique, two-part name for every species the genus and species name, in Latin or Latin-ish. This practice actually started back in the Middle Ages when educated people were expected to know Latin. We know a lot less latin now, but we know a lot more about evolution which Linnaeus didn't. And we have technologies like genetic testing to classify relationships between organisms. And yet we still use Linnaeus's morphology-based system because genetic evidence generally agrees with classifications that are made based on structure and form. However, because there was a lot of life that Linnaeus had no idea about, we had to stick a new taxa above Linnaeus' Kingdom. We call it Domain. And it's as broad as you can get. The Domains are Bacteria, Archaea and Eukarya. The bacteria and archae are prokaryotes, meaning their genetic material goes commando with no nucleus to enclose it. While the Eukarya make up all the life forms with a nucleus and include pretty much all the life that you think of as life, and quite a lot of the life that you don't think about at all. It might seem like, since all macroscopic life only gets one domain, it's kinda silly to give prokaryotes two and for a long time, we didn't. We didn't divide them up into different domains. They hung out together in a single domain called Monera. But it later became clear that Bacteria, which live pretty much everywhere on earth, including inside of you and deep in the Earth's crust, and Archaea which are even more hardy than bacteria, have distinct evolutionary histories. Archaea being more closely related to eukaryotes and, yes, thus me and you. They have totally different cell membranes and the enzymes they use to make RNA, their RNA polymerase, is much more like ours. Under the domain Eukarya, which is by far the most interesting and even occasionally adorable domain, we have Kingdoms: Protista, Fungi, Plantae and Animalia. Now, scientists have settled on these four. For now. But these are categories that are a human creation, but there are good reasons for that human creation. The unscientific truth is that we looked at life and divided it up based on what we saw. So we were like, "Well, protists are single-celled organisms, so, they're very different from the rest of the domain. Plants get their energy from the sun and fungi look and act very different from plants and animals, and we already know what animals are, so they have to get their own kingdom." And though scientists are loathe to admit it, that system of just looking and dividing things up actually worked pretty well for us. Not perfectly, but pretty well. But there's a reason why this worked so well. Evolutionarily, there are actual categories. Each of these kingdoms is a huge branch in the tree of life. At each branch, an evolutionary change occurred that was so massively helpful that it spawned a vast diversity of descendents. Plants or Plantae are the autotrophs of the Domain Eukarya. Autotrophs meaning that they can feed themselves, through photosynthesis of course. Their cellulose-based cell walls and chloroplasts giving them a distinct difference from all other multi-cellular life. There are two other sorts of -trophs. The heterotrophs, which get their energy by eating other organisms. And Chemotrophs, which are weird and crazy and only show up in bacteria and achaea, and they get their energy from chemicals. Now the kingdom Protista is weird because it contains both autotrophs and heterotrophs. Some protists can photosynthesize, while others eat living things. Protists are basically a bunch of weird, eukaryotic single-celled organisms that may or may not be evolutionarily related to each other scientists are still trying to figure it out. Some are plant-like, like algae, some are more animal-like, like amoebas, and some are fungus-like, like slime molds. Protists are one of those gray areas I was telling you about. So don't be surprised if, by the time you're teaching this to your biology students, there are more than four kingdoms in Eukarya. Fungi, which are, you know—the funguses. They include mushrooms, smuts, puffballs, truffles, molds, and yeasts and they're pretty cool because they have cell walls like plants, but instead of being made of cellulose, they're made of another carbohydrate called chitin, which is also what the beak of a giant squid is made out of, or the exoskeleton of a beetle. Because fungi are heterotrophs like animals, they have these sort of digestive enzymes that break down their food and get reabsorbed. But they can't move, they don't require a stomach for digestion they just grow on top of whatever it is they're digesting and digest it right where it is. Which is super convenient! And finally, we have Kingdom Animalia. Which is the lovely kingdom that we find ourselves and 100% of adorable organisms in. Animals are multicellular, always. We're heterotrophic, so we spend a lot of our time hunting down food because we can't make it ourselves. Almost all of us can move, at least during some stage of our life cycle. And most of us develop either two or three germ layers during embryonic development, wait for it... ...unless you're a sponge. So like I said, we use this taxonomic system to describe the common ancestry and evolutionary history of an organism. Looking at the phylogenetic tree, you can tell that humans are more closely related to mice than we are to fish, and more closely related to fish than we are to fruit flies. So how about we pick an organism and follow it all the way through the taxa, from kingdom to species, just to see how it works. I know! Let's pick this kitty. Because I know she'd like it. Right, cat? So, kitties have cells that have nuclei and membrane surrounded organelles. And they're multicellular and heterotrophic and have three germ layers of cells when they're embryos, so they're in the kingdom Animalia. And they have a spinal cord running down their backs, protected by vertebrae, and disks in between them. And they have a tail that doesn't have a butthole at the end of it like a worm, which I'm really glad about. And that puts her in the phylum Chordata. Kitty clearly does not like this, so I'm going to put her down now. And the kitty lactates and gives birth to young like a cow, instead of laying eggs like a chicken, and they have fur and three special tiny bones in their ears that only mammals have, so they're in the class Mammalia. So, she is more closely related to a cow than a chicken. Good to know! And like a bunch of other placental mammals that eat meat like weasels (the mustelids), and dogs, (the canines), kitties are in the order Carnivora. And they're in the cat family, Felidae, whose members have lithe bodies and roundish heads and, except for cheetahs, retractable claws. And they're littler than tigers and panthers, which puts them in the genus Felis. And then, at the level of the species, the descriptions get pretty dang detailed, so let's just say that, you know what a cat is right? So the species name is catus. And look at that: Felis catus! Aw. Kitty. I could have that whole thing cross-stitched onto a pillow for you to sleep on! And it would be cute! Thank you for watching our taxider- I mean, our taxonomy episode of Crash Course Biology. We hope that you learned something. Thanks to everybody who helped put this episode together. If you have any questions for us, please leave them on Facebook or Twitter or in the comments below. And we will get to them. Hopefully very quickly. I will see you next time!

Tree

The tree was created by maximum likelihood analysis without bootstrap: consequently accuracy is traded off for size and many phylum level clades are not correctly resolved (such as the Firmicutes). (Eukaryotes not present in analysis). This 16S rRNA-based phylogenetic tree is based on the ARB-SILVA release LTPs 121 (June 2015)[4][5] and contains all type species with validly published names.


Domain Archaea

Thaumarchaeota

Crenarchaeota (Thermoprotei)

Euryarchaeota

Methanopyrus kandleri

Methanococcales

Eurythermea

Thermococcaceae

Thermoplasmata

Neobacteria

Methanobacteriales

Archaeoglobaceae

Halomebacteria

Methanomicrobia

Halobacteriaceae

Domain Bacteria

Thermotogales

Thermodesulfobiaceae (Firmicutes)

Synergistaceae {Clostridiales Family XV Incertae Sedis} (Firmicutes)

Caldisericum exile

Thermodesulfobacteriaceae

Aquificales

Firmicutes

Thermaerobacter

Caldicellulosiruptor

Thermoanaerobacteraceae

Thermanaeromonas toyohensis

Dictyoglomus

Thermoanaerobacterales Unnamed clade I (incl. Fervidicola)

Thermoanaerobacterales Unnamed clade II

Gelria glutamica

Clostridiales Family XVIII Incertae Sedis

Sulfobacillus

Clostridia s.s. (incl. Thermolithobacter, Negativicutes & Thermoanaerobacterales Unnamed clade III)

Bacilli (incl. Erysipelotrichia & Mollicutes)

Actinobacteria

Chloroflexi

Thermoflexus hugenholtzii

Dehalococcoidaceae

Caldilineaceae

Ardenticatena maritima

Anaerolineaceae

Ktedonobacteria

Thermomicrobia

Chloroflexi

Nitrospiraceae

Deinococci

Thermoanaerobaculum aquaticum

Caldithrix

Gemmatimonas aurantiaca

Fibrobacter

Planctobacteria
Planctomycetes

Phycisphaera mikrensis

Planctomycetales

Chlamydiales

Lentisphaerae

Oligosphaera ethanolica

Lentisphaeria

Verrucomicrobia

Opitutae

Verrucomicrobiales

Sphingobacteria
Chlorobi

Ignavibacteriaceae

Chlorobiaceae

Bacteroidetes

Thiobacteria

Deltaproteobacteria

Deferrisoma carnini

Desulfovibrionales

Desulfurellaceae

Epsilonproteobacteria

Acidobacteria

Holophagae

Bryobacter aggregatus

Acidobacteriaceae

Chrysiogenaceae

Deferribacteraceae

Spirochaetales

Fusobacteriales

Elusimicrobium minutum

Armatimonadetes

Mariprofundus ferrooxydans

Rhodobacteria

Alphaproteobacteria

Chromatibacteria

Gammaproteobacteria (paraphyletic)

Betaproteobacteria

References

  1. ^ Yarza, P.; Richter, M.; Peplies, J. R.; Euzeby, J.; Amann, R.; Schleifer, K. H.; Ludwig, W.; Glöckner, F. O.; Rosselló-Móra, R. (2008). "The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains". Systematic and Applied Microbiology. 31 (4): 241–250. doi:10.1016/j.syapm.2008.07.001. PMID 18692976.
  2. ^ Yarza, Pablo; Ludwig, Wolfgang; Euzéby, Jean; Amann, Rudolf; Schleifer, Karl-Heinz; Glöckner, Frank Oliver; Rosselló-Móra, Ramon (2010). "Update of the All-Species Living Tree Project based on 16S and 23S rRNA sequence analyses". Systematic and Applied Microbiology. 33 (6): 291–299. doi:10.1016/j.syapm.2010.08.001. PMID 20817437.
  3. ^ Munoz, R. L.; Yarza, P.; Ludwig, W.; Euzéby, J.; Amann, R.; Schleifer, K. H.; Oliver Glöckner, F.; Rosselló-Móra, R. (2011). "Release LTPs104 of the All-Species Living Tree". Systematic and Applied Microbiology. 34 (3): 169–170. doi:10.1016/j.syapm.2011.03.001. PMID 21497273.
  4. ^ "ARB-SILVA release LTPs 121: overview" (PDF).
  5. ^ "ARB-SILVA release LTPs 121: full tree" (PDF).

External links

This page was last edited on 1 April 2018, at 22:06
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