Assembling, Visualizing, and Analyzing the Tree of Life

Tree of Life: Are big changes looming on the horizon?

All species like some gadgets

Photo by PublicDomainPictures (Creative Commons Deed CC0)While movie hero James Bond gets his spy gadgets from his loyal developer Q, almost every other species on Earth has to put a little more effort in armoring themselves. But that does not mean they cannot rely on some good ol’ friends to do so. In fact, the acquisition of genes from two or more species through lateral gene transfer can lead to innovations that at times can be painful—sometimes even deadly—to others.

One of those evolutionary novelties is noticeable for certain types of jellyfish that developed the ability to sting after their ancestors acquired a gene from a bacterium and incorporated that material in their own DNA. This gene transmission helped jellyfish to create an innovative defense tool to fend off other species that could endanger them. The result is quite frightening: more humans get killed by jellyfish than sharks.

“It’s no real tree in the classic sense. It’s more like a network.”

Bacterial antibiotic resistance is another threat for humans caused by lateral gene transfer, also called horizontal gene transfer, which is the non-genealogical (non-vertical) exchange of genes from one species (lineages) to another that potentially creates new adaptive functions for the recipient. Those transmissions have had a profound effect on the evolution of Bacteria and Archaea, and to a lesser extent Eukaryotes (i.e. cells with nuclei, like our selves).

Importantly, the described changes of those jellyfish happened independently of reproduction and, thus, went beyond the classical Darwinian framework that species descend over time from common ancestors. DNA sequencing has demonstrated that unraveling evolutionary paths depends on close examinations of vertical and lateral events, because divergence is not only caused by inherited changes between parent and offspring.

Spider webs

As anyone in the phylogenetic community can attest, it is already hard enough to provide an adequate estimation of trees by looking at vertical relationships. Let alone, that also numerous lateral events must be taken into account to explain how species have evolved over time. Some scientists question if it is even possible to reconstruct some parts of the tree of life in some acceptable manner because of the ongoing lateral gene transfer.

This has obvious consequences for the investigators of the Open Tree of Life, who are currently developing software and other tools to connect all known species on Earth. “Lateral-gene transfer is going on all the time. There is no real tree in the classic sense. It is more like a network,” says Laura Katz, a professor of biological sciences at Smith College. Hence, the Open Tree of Life project is developing tools to capture and depict representative lateral gene transfer events across the tree of life.

“It looks more like a tree that is covered with spider webs”

Katz maintains that lateral gene transfer is fundamental for the understanding of how many species have evolved over time. Instead of picturing a tree with domains that are separated in three branches, “it looks more like a tree that is covered with a lot of spider webs,” she concludes.

Lateral gene transfers can occur in all directions between the different domains of life, although most documented evidence comes from exchanges between Bacteria and Archaea. It is possible for species to have genetic material that can be traced back to all domains, explains Smith College postdoc researcher Kristen Swithers.

Frankenstein species

Swithers has investigated the lateral gene transfers for the Thermotogae phylum and found for certain species that only about 10 percent of their genes were inherited vertically and not generated through such lateral exchanges. For example, about two-fifth of the genes had been transferred from other bacteria and another 12 percent were similar to genes found in certain types of Archaea. “We call it a Frankenstein species,” she adds. “It has a little bit from everything.”

Those complex investigations are possible because of the rapid advancements in genomic sequencing techniques to compare complete sets of genes from numerous organisms. With those patterns it is possible to match the data with the most-recent phylogenies to examine vertical evolution and to see if there are lateral connections with other species as well. As a result, some parts of the tree of life have already been adjusted because DNA analysis showed that some relations between species are different than initial thought.

“You are what you eat”

“We need to go through the entire tree of life again to see where there are connections that are not vertical,” says Swithers. For many of the Eukaryotes the characteristics that are stored in databases are physical. “There are no sequencing data for them yet, but eventually that will allow for better insight on the relationships, even when they are lateral.”

For instance, such research already has provided evidence that some gut bacteria have borrowed genes from ocean microbes that can break down carbohydrate molecules in seaweed, one of the main ingredients in sushi. Such gut bacteria have been found in the intestines from Japanese individuals, but not in Americans (which, according to Swithers, reinforces the “you are what you eat” saying). Thus, this shows the importance of DNA sequencing data for the understanding of the relationships between species, because seaweed has become a novel carbon source for people with this special gut bacterium—it makes sushi even healthier than it already is.

Isn’t that a gadget that a lot of people would like to have?

Even James Bond would be jealous.

Photo: PublicDomainPictures

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One response

  1. The big question concerning the gene acquired from bacteria is where did the bacteria acquire that full fledged gene from? Is it possible that they some how constructed it them selves?

    January 21, 2013 at 6:51 pm

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