Wednesday, April 8, 2009
What's in a tree of life?
On page 87, Carroll depicts a conventional tree of life. On page 89, he depicts a new tree of life. What are the fundamental differences between these two models of the history of life? How are they the same? How were these trees developed? What do "immortal genes" have to do with the classifications?
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The first classification for the forms of life began with Aristotle, who ~4th century BC divided organisms into two groups, plants and animals and furthered the division of these organisms into “blood” and “bloodless” as well as three groups based on transportation (walking, flying, and swimming) land, air and water. His system was used into the 1600’s, until Carolus Linnaeus developed the two-kingdom classification. The plant and animal kingdoms were then divided into genera (genus) and species. He designated a system of naming organisms called binomial nomenclature that gave a Genus and a Species name to each organism.
ReplyDeleteWhile Linnaeus classified for ease of identification, classification is now widely accepted as a way to trace common descent. This technique is called cladistic taxonomy, where the taxon is arranged in an evolutionary tree. Chatton developed the 2-empire system in 1937, establishing a Prokaryotic and Eukaryotic class. Copeland, in 1956 furthered the division of the Eukaryotes into Protists, Fungi, Plantae, and Animalia and finally Woese divided the prokaryotes into Eubacteria and Archaebacteria.
There are three types of classification: traditional, phentic, and cladistic. Data used in the traditional system stresses both monophylesis (common ancestry) and the amount of divergence amongst the groups. In this case, an “immortal gene” may be considered to be more of a primitive character that is present in one common ancestor and all of the ancestors of that group, such as the amniotic egg. This would then be the basis for the traditional formation of the tree.
Phenetics is the used to classify a group based on the number of their similarities (or in opposition, the number of differences) and traits. There are many problems with this, due to an extreme number of overlaps between organisms.
The Cladistic method groups organisms based on the presence of shared derived characteristics, not the overall similarity of potential group members. For example, the use of feathers and hair to separate birds and mammals from reptiles wouldn’t be a factor in the cladogram, because this factor is only found in one taxon.
http://en.wikipedia.org/wiki/Biological_classification#Early_systems
http://www.usoe.k12.ut.us/CURR/Science/sciber00/7th/classify/sciber/history.htm
Here is a brief history of how our modern tree was developed, and how immortal genes fit into the making of the trees. In Darwin’s time, the living world was divided into two kingdoms: plant and animal. Like Melissa said, this system has been in play since Aristotle, and was formalized by Carl von Linne. Ernst Haeckel, in 1866, added a third kingdom: Protista. Bacteria and fungi were later added on in the twentieth century.
ReplyDeleteThis five kingdom scheme kept everybody happy. In 1938 Edouard Chatton grouped everything into two superkingdoms: prokaryote and eukaryote. These superkingdoms are based solely on the absence and presence of nuclei. These two superkingdoms included every organism in the living world, until Carl Woese started studying the genes of a species that Tom Brock found in Yellowstone.
Carl Woese wanted to determine the evolutionary relationships among species, and to base the trees off that. Instead of using appearance or physical traits, he used molecular traits. He wanted to build species trees using DNA, RNA, and protein sequences. Here is how that works. If two species share a certain text of DNA, they have a degree of kinship. A species that shares a block of DNA with species A but not species B is most likely more related to species A than to species B. Of course, it is more complicated than that. Relationships can become tangled; for example, microbes can exchange genes between distant relatives due to their ability to live within other host species (endosymbiosis). This can confuse a family tree. However, the general thing that scientists look for in a tree is a degree of kinship.
Carl Woese propsed a third superkingdom: archaeabacteria (or simply Archaea). The superkingdom got renamed to domain. Life has since been described as three domains: Eukarya, Archaea, and Bacteria.
Immortal genes can be used to determine degrees of kinship. Here is a simple example mention in the book. Many early studies of archaea and eukaryotes showed that they were similar in many ways. There is a short sequence of amino acids in eukaryotes and Archaea: GEYEAGMSAEG, that is not present in Bacteria. This sequence, being in Archaea and Eukarya, has obviously survived for a long time despite constant bombardment of mutations. It is considered an immortal gene, and is a reliable source to determine degrees of kinship. If this long-lived gene is in both Eukaryotes and Archaea but not in Bacteria, it means that somewhere early along the line Bacteria began to differ from both Archaea and Eukaryotes. This provides a view consistent with the “conventional” tree of life found on page 87, in which Archaea branch off from Eukaryotes, while Eukaryotes and Bacteria have separate branches from LUCA.
Survival of the Fittest
http://en.wikipedia.org/wiki/Carl_Woese
http://en.wikipedia.org/wiki/Kingdom_(biology)
The conventional tree of life on page 87 shows the three domains, Bacteria, Archaea, and Eukarya, branching off from a common universal ancestor. Domain Bacteria branches off first, then Archaea, then Eukarya.
ReplyDeleteHowever, the relationships between the three Domains were brought into question, where evidence provided by genome study showed that Bacteria and Archaea were closely related; then with later research of Eukarya, Archaea and Eukarya were found to be more closely related. Domains Archaea and Eukarya shared similarities in regards to copying and decoding DNA, while Domains Bacteria and Eukarya shared similarities in regards to metabolism. As a result of genome research, the new tree of life was created, where organisms in Domain Eukarya evolved from a combination of the Domain Bacteria and Archaea.
These two trees of life are similar in that they agree that all three Domains share a genetic relationship; but they differ in how the Domain Eukarya came about. The conventional tree depicts Eukarya diverging from an Archaea and Eukarya ancestor, showing an expansive split from Bacteria, whereas the new tree depicts Eukarya emerging from the other domains.
Immortal genes comes into play in these classification trees because the presence of immortal genes in the genome of organisms within a Domain would provide evidence of the relationship between other different domains, and thus a genetic connection supporting the theory of Evolution.