Stochastic Models for Horizontal Gene Transfer: Taking a Random Walk through Tree Space

By Suchard, Marc A. | Genetics, May 2005 | Go to article overview

Stochastic Models for Horizontal Gene Transfer: Taking a Random Walk through Tree Space


Suchard, Marc A., Genetics


ABSTRACT

Horizontal gene transfer (HGT) plays a critical role in evolution across all domains of life with important biological and medical implications. I propose a simple class of stochastic models to examine HGT using multiple orthologous gene alignments. The models function in a hierarchical phylogenetic framework. The top level of the hierarchy is based on a random walk process in "tree space" that allows for the development of a joint probabilistic distribution over multiple gene trees and an unknown, but estimable species tree. I consider two general forms of random walks. The first form is derived from the subtree prune and regraft (SPR) operator that mirrors the observed effects that HGT has on inferred trees. The second form is based on walks over complete graphs and offers numerically tractable solutions for an increasing number of taxa. The bottom level of the hierarchy utilizes standard phylogenetic models to reconstruct gene trees given multiple gene alignments conditional on the random walk process. I develop a well-mixing Markov chain Monte Carlo algorithm to fit the models in a Bayesian framework. I demonstrate the flexibility of these stochastic models to test competing ideas about HGT by examining the complexity hypothesis. Using 144 orthologous gene alignments from six prokaryotes previously collected and analyzed, Bayesian model selection finds support for (1) the SPR model over the alternative form, (2) the 16S rRNA reconstruction as the most likely species tree, and (3) increased HGT of operational genes compared to informational genes.

TRADITIONAL views of molecular evolution hold that genetic material mutates slowly over time as it is passed in a vertical fashion from parent to progeny. Molecular phylogenetics then aims to reconstruct this history of inheritance of genetic sequence data from contemporary organisms into a tree-like structure. However, belief in a single tree, mandated by vertical transmission, for all genetic material is changing. Evolutionary biologists increasingly recognize the horizontal transmission of genetic material between distantly related organisms as an important mechanism of evolution (SYVANEN 1994; LAWRENCE 1999; JAIN et al 2002).

The process of horizontal (or lateral) gene transfer (HGT) plays a critical role across all domains of life and in particular among prokaryotes QAIN et al. 1999; KOONIN et al. 2001). For example, many prokaryotes are agile at quickly adapting to new environments. Often, this ability stems from the acquisition of new genes through HGT rather than through random mutation (LAWRENCE 1999). At least three mechanisms promote HGT in prokaryotes QAIN et al. 2002). These include: (1) transformation in which free DNA sequences are absorbed from the environment, (2) conjugation between two different prokaryotic species, and (3) transduction of genetic material through viruses. Finally, HGT also has medical importance (BROWN 2003). In the field of infectious diseases, HGT among bacterial pathogens of antibiotic resistance genes has greatly contributed to the emergence of multidrug-resistant bacteria in clinical settings (LEVERSTEIN-VAN HALL et al. 2002). In the field of oncology, HGT may also affect tumor progression; BERGSMEDH et al. (2001) show that eukaryotic cells can transfer active oncogenes.

Three general methods have been employed to examine HGT. The first focuses on single genomes and identifies genes suspected to have been imported through HGT by examining variation in nucleotide base composition and codon usage patterns (LAWRENCE and OCHMAN, 1997). The latter two methods are comparative studies across species. One uses similarity approaches based on gene content to identify HGT (RAGAN 2001) and to propose average genome or species-level trees (SNEL et al. 1999), while the alternative method endorses phylogenetic reconstruction using orthologous genes (JAIN et al. 1999). Base composition and codon bias studies may perform poorly when compared to phylogenetic methods (KoSKi et al. …

The rest of this article is only available to active members of Questia

Sign up now for a free, 1-day trial and receive full access to:

  • Questia's entire collection
  • Automatic bibliography creation
  • More helpful research tools like notes, citations, and highlights
  • Ad-free environment

Already a member? Log in now.

Notes for this article

Add a new note
If you are trying to select text to create highlights or citations, remember that you must now click or tap on the first word, and then click or tap on the last word.
One moment ...
Default project is now your active project.
Project items

Items saved from this article

This article has been saved
Highlights (0)
Some of your highlights are legacy items.

Highlights saved before July 30, 2012 will not be displayed on their respective source pages.

You can easily re-create the highlights by opening the book page or article, selecting the text, and clicking “Highlight.”

Citations (0)
Some of your citations are legacy items.

Any citation created before July 30, 2012 will labeled as a “Cited page.” New citations will be saved as cited passages, pages or articles.

We also added the ability to view new citations from your projects or the book or article where you created them.

Notes (0)
Bookmarks (0)

You have no saved items from this article

Project items include:
  • Saved book/article
  • Highlights
  • Quotes/citations
  • Notes
  • Bookmarks
Notes
Cite this article

Cited article

Style
Citations are available only to our active members.
Sign up now to cite pages or passages in MLA, APA and Chicago citation styles.

(Einhorn, 1992, p. 25)

(Einhorn 25)

1

1. Lois J. Einhorn, Abraham Lincoln, the Orator: Penetrating the Lincoln Legend (Westport, CT: Greenwood Press, 1992), 25, http://www.questia.com/read/27419298.

Cited article

Stochastic Models for Horizontal Gene Transfer: Taking a Random Walk through Tree Space
Settings

Settings

Typeface
Text size Smaller Larger Reset View mode
Search within

Search within this article

Look up

Look up a word

  • Dictionary
  • Thesaurus
Please submit a word or phrase above.
Print this page

Print this page

Why can't I print more than one page at a time?

Full screen

matching results for page

Cited passage

Style
Citations are available only to our active members.
Sign up now to cite pages or passages in MLA, APA and Chicago citation styles.

"Portraying himself as an honest, ordinary person helped Lincoln identify with his audiences." (Einhorn, 1992, p. 25).

"Portraying himself as an honest, ordinary person helped Lincoln identify with his audiences." (Einhorn 25)

"Portraying himself as an honest, ordinary person helped Lincoln identify with his audiences."1

1. Lois J. Einhorn, Abraham Lincoln, the Orator: Penetrating the Lincoln Legend (Westport, CT: Greenwood Press, 1992), 25, http://www.questia.com/read/27419298.

Cited passage

Welcome to the new Questia Reader

The Questia Reader has been updated to provide you with an even better online reading experience.  It is now 100% Responsive, which means you can read our books and articles on any sized device you wish.  All of your favorite tools like notes, highlights, and citations are still here, but the way you select text has been updated to be easier to use, especially on touchscreen devices.  Here's how:

1. Click or tap the first word you want to select.
2. Click or tap the last word you want to select.

OK, got it!

Thanks for trying Questia!

Please continue trying out our research tools, but please note, full functionality is available only to our active members.

Your work will be lost once you leave this Web page.

For full access in an ad-free environment, sign up now for a FREE, 1-day trial.

Already a member? Log in now.