Papers by Dr Michael Syvanen on Horizontal Gene Transfer UC Davis Department of Microbiology, University of California


List of papers for which reprints are no longer available.

The following papers are covered by copyrights. You are free to download single copies of any of these papers for your own private use, study or research. Reproduction of this material is confined to the purpose for which permission is hereby given and excludes use in any electronic form other than on the World Wide Web as specified above. This permission is granted for non-exclusive world English rights only. For other languages please reapply separately for each one required. The papers are not to be reproduced for broad and/or commercial distribution. Permission will be granted for reproduction for course work by contacting the author.

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  1. Journal Theoretical Biology v 112 pp 333-343 [1985]
  [ PDF ] [ Notes ]
  1. Journal Theoretical Biology v 107 pp 685-696 [1984]
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  1. Trends In Genetics pp 1-4 [1986]
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  1. Journal of Molecular Evolution v 26 pp 16-23 [1987]
  [ PDF ] [ Notes ]
  1. Journal of Molecular Evolution v28 pp536-544 [1989]
  [ PDF ] [ Notes ] Posted 11/01
  1. Cell v 60 pp 7-8 [1990]
  [ PDF ] [ Notes ] Posted 11/01
  1. AnnuRevGen v 28 pp 237-261 [1994]
  [ PDF ] [ Notes ]
  1. Trends in Genetics v18 no.5 pp 245-248 [2002]
  [ PDF ] [ Notes ] Posted 06/02
  1. Journal of Molecular Evolution v 54 pp 258-266 [2002]
  [ PDF ] [ Notes ] Posted 12/02
  1. Journal of Molecular Evolution v 55 pp 85-91 [2002]
  [HTML] [ Notes ] Posted 12/02
  1. Horizontal Gene Transfer. pp 383 - 395. [2002]
  [ PDF ] [ Notes ] Posted 12/04
  1. Some Computational Problems Associated with Horizontal Gene Transfer. pp 248 - 268. [2005]
  [ PDF ] [ Notes ] Posted 09/07



 

Full reference and notes.

1. Michael Syvanen. 1985. Cross-species Gene Transfer;      
Implications for a New Theory of Evolution.
J. Theor. Biol. 112: 333—343.
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Note: This is the first paper I wrote on the subject of horizontal gene transfer. It addresses the following subjects: why the genetic code is uniform, why von Baer's Law, parallelisms, and radiations in the fossil record.


 


2. Michael Syvanen. 1984. Conserved Regions in Mammalian
ß-globins: Could They Arise by Cross-species Gene
Exchange?   J. Theor. Biol. 107: 685—696.
  [ PDF ] [ Index ] 
Note: This is the first molecular evolution analysis I performed testing the hypothesis of horizontal gene transfer as a major force in evolution. This paper addresses whether or not neutral substitutions across the ß-globin gene are randomly distributed. It finishes with a theory as to the evolutionary function of introns.


 


3. Michael Syvanen. 1986. Cross-species gene transfer:
a major factor in evolution?   Trends In Genetics pp 1—4.
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Note: Just a short review that summarizes the two above papers [ 1 ]
[ 2 ] and ends with some speculations on protozoan evolution.

 


 


4. Michael Syvanen. 1987. Molecular Clocks and
Evolutionary Relationships: Possible Distortions Due          
to Horizontal Gene Flow.   J. Mol. Evol. 26: 16—23.
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Note: This paper presents a general discussion of the overall patterns of molecular evolution if horizontal gene transfer was a major force. It deals mostly with metazoan evolution from the point of view that viruses are major vectors of gene transfer.


 


5. Michael Syvanen, Hyman Hartman and Peter F. Stevens.
1989. Classical Plant Taxonomic Ambiguities Extend
to the Molecular Level. J. Mol. Evol. 28:536-544.
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Note: At the request of the late Allan C. Wilson, then editor of JME, we removed the discussion of horizontal gene transfer from this paper. Hence, I incorporated the discussion of the theoretical implications of this paper in a later review [ see below, paper 7 ]. The paper shows, as stated in the title, that homoplasy in plant evolution is more extensive than with animal evolution. And molecular data will not rescue the situation. With the accumulation of more recent plant sequences the problem of homoplasy remains.


 


6. Michael Syvanen. 1990. Migrant DNA in the Bacterial
World. Cell 60: 7-8.
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Note: This is a short review of the book “Gene Transfer in the Environment”. It is included in this list because I explicitly address the issue of the whether the phenomena of reproductive isolation and the general pattern of nested hierarchies observed in taxonomy precludes a rate of horizontal gene transfer that could significantly influence macroevolutionary trends.


 


7. Michael Syvanen. 1994. Horizontal Gene Transfer:          
Evidence and Possible Consequences.  
Annu. Rev. Genet. 28: 237—61.
  [ PDF ] [ Index ]
Note: This is a general review of horizontal gene transfer... could be subtitled "what the Russians discovered" from Vavilov to Krassilov. The main issue addressed here is how to identify a possible gene transfer event from comparative sequence analysis. This includes criteria for identification with many examples of artifactual identifications. In addition, a strong case is made that angiosperm evolution is heavily influenced by horizontal gene transfer.


 


8. Michael Syvanen. 2002. Recent emergence of the           
modern genetic code: a proposal.  
Trends Genet. 18 (5): 245-8.
  [ PDF ] [ Index ]
Note: This paper is an extension of ideas presented in paper #1 on the unity of the genetic code. A strong argument is presented that not only did the genetic code continue to evolve after diversification of life's three major kingdoms but that also the entity, commonly referred to as the Last Common Ancestor, was actually a collection of disparate genetic lineages.

Reprinted at this web site with permission from Elsevier Science. The Trends in Genetics homepage is at: www.trends.com



9. Michael Syvanen. 2002. On the Occurance of           
Horizontal Gene Transfer Among an Arbitrarily Chosen
Group of 26 Genes.   J. Mol. Evol. 54:258-266.
  [ PDF ] [ Index ]
Note: This paper describes an analysis that began as an attempt to determine which fraction of genes common to Bacteria, Archaea and Eukaryotes supported the universal tree (Archaea and Eukaryotes as closest relatives) as opposed to those that do not. In the course of the analysis, a group of genes were selected that had high levels of similarity to each other -- this lead to a result that was initially surprising. Paper 8 was originally the discussion for this paper, but the editors suggested it be removed as being too speculative.


10. Michael Syvanen. 2002. Rates of Ribosomal RNA           
Evolution Are Uniquely Accelerated in Eukaryotes.
J. Mol. Evol. 55:85-91.
  [ HTML ] [ Index ]
Note: This paper describes the distance matrix rate test, a tool that can be used to illustrate horizontal gene transfer events (as shown in paper 9), but otherwise does not address this topic. This paper ends with the suggestion that the highly variable rates of evolution observed with the Eukaryotic ribosomal RNA genes is a consequent of the hypothesized longevity sensor that possibly resides in these genes.


11. Michael Syvanen. 2002. Temporal patterns of plant and
metazoan evolution suggest extensive polyphyly. In
Horizontal Gene Transfer 2nd Ed. Edited by
Michael Syvanen and Clarence Kado. Academic Press,
London. pp 383 - 395.
  [ PDF ] [ Index ]
Note: This paper is not available elsewhere through electronic publishing. Ribosomal RNA sequences are used to obtain molecular distances that are used to estimate divergence times. This work shows that many major clades (angiosperm families and three metazoan groups) arose at times significantly earlier than is indicated by the fossil record. This is further evidence that major evolutionary radiations were possibly accompanied by extensive horizontal gene transfers.


12. Michael Syvanen. 2005.
Some Computational Problems Associated with Horizontal
Gene Transfer. Genomics pp. 248-268.
  [ PDF ] [ Index ]
First Paragraph: It has been over 30 years since the suggestion that horizontal gene transfer (HGT) may have been a factor in the evolution of life entered the literature. Initially these speculations were based on discoveries made in medical microbiology, namely, that genes for resistance to antibiotics were found to move from one bacterial pathogen to another. This discovery was so unexpected and contrary to accepted genetic principles that though it was announced in Japan in 1959 [1,2], it was not generally recognized in the West for another decade. Speculations that HGT may have been a bigger factor in the evolution of life was inviting because it offered broad explanations for a variety of biologi- cal phenomena that have interested and puzzled biologists for over the last century and a half, These were problems that had been raised by botanists who have puzzled over the evolution of green plants 131 as well as by paleontologists who recorded macroevolutionary trends [4] in the fossil record that were often difficult to reconcile with the New Synthesis that merged Darwin's thinking with Mendelian genetics. However, outside of the field of bacteriology this exercise did not really attract that much attention until the late 1990s, at which time there was a major influx of data indicating that HGT had been very pervasive in early life. Namely, complete genome sequences began to appear. Simple examination of these sequences showed beyond any doubt that horizontal gene transfer was indeed a major factor in the evolution of modern bacterial, archaeal, and eukaryotic genomes.



 
Horizontal Gene Transfer 2nd Ed. In 2002 Academic Press published a collection of reviews and original research articles covering some of the most recent findings and insights into horizontal gene transfer. This is editied by myself and Clarence Kado.

Horizontal gene transfer is the transfer of genetic material between distinct species, a process that plays a major role in the evolution of the genome. Evidence for the transfer of genes singly and in modular groups between lower and higher organisms (including humans) has been mounting. The second edition of Horizontal Gene Transfer has been organized to provide a concise and up-to-date coverage of the most important discoveries in this fascinating field. Written by the most prominent gene transfer and genome analytical scientists, this book details experimental evidence for the phenomenon of horizontal gene transfer and discusses further evidence provided by the recent completion of genomic sequences from Archea, Bacteria, and Eucarya members.

[ Click Here to Order On-line ]
 

 
     
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