Papers on horizontal gene transfer by Michael Syvanen, PhD ( UC Davis, CA)

Papers by Dr Michael Syvanen on Horizontal Gene Transfer

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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Journal Theoretical Biology v 112 pp 333-343 [1985]
[ PDF ] [ Notes ]

AnnuRevGen v 18 pp 271-293 [1984]
[ PDF ] [ Notes ] Posted 09/12

Journal Theoretical Biology v 107 pp 685-696 [1984]
[ PDF ] [ Notes ]

Trends In Genetics pp 1-4 [1986]
[ PDF ] [ Notes ]

Journal of Molecular Evolution v 26 pp 16-23 [1987]
[ PDF ] [ Notes ]

Journal of Molecular Evolution v28 pp536-544 [1989]
[ PDF ] [ Notes ] Posted 11/01

Cell v 60 pp 7-8 [1990]
[ PDF ] [ Notes ] Posted 11/01

AnnuRevGen v 28 pp 237-261 [1994]
[ PDF ] [ Notes ]

Trends in Genetics v18 no.5 pp 245-248 [2002]
[ PDF ] [ Notes ] Posted 06/02

Journal of Molecular Evolution v 54 pp 258-266 [2002]
[ PDF ] [ Notes ] Posted 12/02

Journal of Molecular Evolution v 55 pp 85-91 [2002]
[HTML] [ Notes ] Posted 12/02

Horizontal Gene Transfer. pp 383 - 395. [2002]
[ PDF ] [ Notes ] Posted 12/04

Some Computational Problems Associated with Horizontal Gene Transfer.
pp 248 - 268. [2005]
[ PDF ] [ Notes ] Posted 09/07

J Biological Systems, Vol. 18, No. 2: 261–275 [2010]
[ PDF ] [ Notes ] Posted 07/10

AnnuRevGen, Vol. 46: 341-358 [2012]
[HTML] [ Notes ] Posted 09/12

Evolutionary Biology: Genome Evolution, Speciation, Coevolution and Origin of Life, pp 191-205 [2014]
[PDF] [ Notes ] Posted 12/15

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.	[ PDF ] [ Index ]
	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. The evolutionary implications of mobile genetic elements. Annual Review Genetics. 18:271-93.	[ PDF ] [ Index ]
	Note: New posting September 6, 2012. This contains the first paper where the more theoretical aspects of horizontal gene transfer are outlined by the author. A major theme of this review is to make the case for mobile genetic elements and other mechanisms that promote horizontal gene transfer being shaped by the forces of natural selection via their ability to promote beneficial phenotypes. Or as has been said elsewhere: life has evolved to evolve.

3.	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.

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

5.	Michael Syvanen. 1987. Molecular Clocks and Evolutionary Relationships: Possible Distortions Due to Horizontal Gene Flow. J. Mol. Evol. 26: 16—23.	[ PDF ] [ Index ]
	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.

6.	Michael Syvanen, Hyman Hartman and Peter F. Stevens. 1989. Classical Plant Taxonomic Ambiguities Extend to the Molecular Level. J. Mol. Evol. 28:536-544.	[ PDF ] [ Index ]
	Note: At the request of the late Allan C. Wilson, then editor of JME, we removed the discussion of horizontal gene transfer [ lateral gene transfer ] from this paper. Hence, I incorporated the discussion of the theoretical implications of this paper in a later review [ see below, paper 8 ]. 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.

7.	Michael Syvanen. 1990. Migrant DNA in the Bacterial World. Cell 60: 7-8.	[ PDF ] [ Index ]
	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.

8.	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 [ lateral gene transfer ] ... 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. This is includes an early review of those regions of bacterial chromosomes that are now called genomic islands and are central to understanding the concept of the pangenome. In addition, a case is made that angiosperm evolution is heavily influenced by horizontal gene transfer [ lateral gene transfer ].

9.	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

10.	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.

11.	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.

12.	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.

13.	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.

14.	Michael Syvanen and Jonathan Ducore. 2010. Whole genomoe comparrisons reveals a possible chimeric origin for a major metazoan assemblage. Journal of Biological Systems, Vol. 18, No. 2: 261–275	[ PDF ] [ Index ]
	Note: This paper is presented here with permission from "World Scientific Publishing Co. Pte. Ltd." They are the publisher and can be found at www.wspc.com. Abstract: The availability of whole genome sequences from multiple metazoan phyla is making it possible to determine their phylogeny. We have found that a sea urchin and human define a clade that excludes a tunicate, contradicting both classical and recent molecular studies that place the tunicate and vertebrate in the Chordate phylum. Intriguingly, by means of a novel four taxa analysis, we have partitioned the 2000 proteins responsible for this assignment into two groups. One group, containing about 40% of the proteins, supports the classical assemblage of the tunicate with vertebrates, while the remaining group places the tunicate outside of the chordate assemblage. The existence of these two phylogenetic groups is robustly maintained in five, six and nine taxa analyses. These results suggest that major horizontal gene transfer events occurred during the emergence of one of the metazoan phyla. The simplest explanation is that the modern tunicate (as represented by Ciona intestinalis) began as a hybrid between a primitive vertebrate and some other organism, perhaps from an extinct and unidentified protostome phylum, at a time close to but after the diversification of the chordates and echinoderms and before the lineages leading to Drosophila melanogaster and Caenorhabditis elegans diverged. Keywords: Horizontal Gene Transfer; Four-Taxa Analysis; Tunicate; Chordate; Protostome; Deuterostome.

15.	Michael Syvanen. 2012. Evolutionary Implications of Horizontal Gene Transfer. Annual Review of Genetics Vol. 46: 341-358.	[ HTML ] [ Index ]
	Note: This latest review describes how horizontal gene transfer can change our thinking about such things as the tree of life, the notion of a last universal common ancestor,the biological unities, rules of taxonomic nomenclature, an unexpected support for Muller’s ratchet and the bacterial pangenome. The emergence of the eukaryotic cell and the occurrence of HGT among metazoan phyla involving both transposable elements and structural genes for normal housekeeping functions. Abstract: The flow of genes between different species represents a form of genetic variation whose implications have not been fully appreciated. Here I examine some key findings on the extent of horizontal gene transfer (HGT) revealed by comparative genome analysis and their theoretical implications. In theoretical terms, HGT affects ideas pertaining to the tree of life, the notion of a last universal common ancestor, and the biological unities, as well as the rules of taxonomic nomenclature. This review discusses the emergence of the eukaryotic cell and the occurrence of HGT among metazoan phyla involving both transposable elements and structural genes for normal housekeeping functions. I also discuss the bacterial pangenome, which provides an important case study on the permeability of species boundaries. An interesting observation about bdelloid rotifers and their reversion to asexual reproduction as it pertains to HGT is included.

16.	Michael Syvanen , Bryan Ericksen, Simone Linz, Jonathan Ducore. 2014. Quartet Partitioning Reveals Hybrid Origins of the Vertebrate. Evolutionary Biology: Genome Evolution, Speciation, Coevolution and Origin of Life pp 191-205.	[ PDF ] [ Index ]
	Note: This Note from the Author, Michael Syvanen, is being prepared for this site. Abstract: It is generally accepted that humans and sea urchins are deuterostomes and that fruit flies and jelly fish are outgroups. However, when we analyzed proteins from the genomes of these four species and submitted them to 4 taxa phylogenetic analysis, we found that, while as expected, most of the proteins (563) supported the notion of human and sea urchin in one clade and jelly fish and fruit flies in the other clade (Tree1), a large number of proteins (353) showed human and fruit fly in one clade with the sea urchin and jelly fish in the other (Tree3). Homologs were found in the genomes from 5 other metazoa. Tree1 proteins resulted in the expected 9 taxa tree, while the Tree3 proteins show vertebrates, to the exclusion of the other chordates, in the protostome clade. The two 9 taxa trees were fused into a single most parsimonious net that supports an introgression event between a vertebrate ancestor and a primitive protostome.

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.

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