TITLE

On the need for integrative phylogenomics, and some steps toward its creation

AUTHOR(S)
Bapteste, Eric; Burian, Richard M.
PUB. DATE
September 2010
SOURCE
Biology & Philosophy;Sep2010, Vol. 25 Issue 4, p711
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Recently improved understanding of evolutionary processes suggests that tree-based phylogenetic analyses of evolutionary change cannot adequately explain the divergent evolutionary histories of a great many genes and gene complexes. In particular, genetic diversity in the genomes of prokaryotes, phages, and plasmids cannot be fit into classic tree-like models of evolution. These findings entail the need for fundamental reform of our understanding of molecular evolution and the need to devise alternative apparatus for integrated analysis of these genomes. We advocate the development of integrative phylogenomics for analyzing these genomes and their histories, with tools suited to analyzing the importance of lateral gene transfer (LGT) and of DNA evolution in extra-cellular mobile genetic elements (e.g., viruses, plasmids). These phenomena greatly increase the complexity of relationships among interacting genetic partners, as they exchange functional genetic units. We examine the ontology of functional genetic units, interacting genetic partners, and emergent genetic associations, argue that these three categories of entities are required for a successful integrated phylogenomics. We conclude with arguments to suggest that the proposed new perspective and associated tools are suitable, and perhaps required, as a replacement for the bifurcating trees that have dominated evolutionary thinking for the last 150 years.
ACCESSION #
53021205

 

Related Articles

  • The Repetitive DNA Elements Called CRISPRs and Their Associated Genes: Evidence of Horizontal Transfer Among Prokaryotes. Godde, James S.; Bickerton, Amanda // Journal of Molecular Evolution;Jun2006, Vol. 62 Issue 6, p718 

    We have found direct DNA repeats 21–47 bp in length interspersed with nonrepetitive sequences of similar length, or clustered regularly interspaced short palindromic repeats (CRISPRs) in a wide range of diverse prokaryotes, including many Archaeal and Eubacterial species. A number of cas,...

  • Neutral Evolution of Ten Types of mariner Transposons in the Genomes of Caenorhabditis elegans and Caenorhabditis briggsae. Witherspoon, David J.; Robertson, Hugh M. // Journal of Molecular Evolution;Jun2003, Vol. 56 Issue 6, p751 

    Ten types of mariner transposable elements (232 individual sequences) are present in the completed genomic DNA sequence of Caenorhabditis elegans and the partial sequence of Caenorhabditis briggsae. We analyze these replicated instances of mariner evolution and find that elements of a type have...

  • Natural Plasmid Transformation in Escherichia coli. Suh-Der Tsen, Sue-Jean; Suh-Sen Fang, Sue-Jean; Mei-Jye Chen, Sue-Jean; Jun-Yi Chien, Sue-Jean; Chih-Chun Lee, Sue-Jean; Han-Lin Tsen, Darwin // Journal of Biomedical Science;2002, Vol. 9 Issue 3, p246 

    Although Escherichia coli does not have a natural transformation process, strains of E. coli can incorporate extracellular plasmids into cytoplasm ‘naturally’ at low frequencies. A standard method was developed in which stationary phase cells were concentrated, mixed with plasmids,...

  • Influence of industrial contamination on mobile genetic elements: class 1 integron abundance and gene cassette structure in aquatic bacterial communities. Wright, Meredith S.; Baker-Austin, Craig; Lindell, Angela H.; Stepanauskas, Ramunas; Stokes, Hatch W.; McArthur, J. Vaun // ISME Journal: Multidisciplinary Journal of Microbial Ecology;Arp2008, Vol. 2 Issue 4, p417 

    The acquisition of new genetic material via horizontal gene transfer allows bacteria to rapidly evolve. One key to estimating the contribution of horizontal gene transfer to bacterial evolution is to quantify the abundance of mobile genetic elements (MGEs) in bacterial communities under varying...

  • The role of conjugative transposons in spreading antibiotic resistance between bacteria that inhabit the gastrointestinal tract. Scott, K. P. // Cellular & Molecular Life Sciences;Dec2002, Vol. 59 Issue 12, p2071 

    There is huge potential for genetic exchange to occur within the dense, diverse anaerobic microbial population inhabiting the gastrointestinal tract (GIT) of humans and animals. However, the incidence of conjugative transposons (CTns) and the antibiotic resistance genes they carry has not been...

  • Comparison of SXT and R391, two conjugative integrating elements: definition of a genetic backbone for the mobilization of resistance determinants. Beaber, J. W.; Burrus, V.; Hochhut, B.; Waldor, M. K. // Cellular & Molecular Life Sciences;Dec2002, Vol. 59 Issue 12, p2065 

    The SXT element (SXT) is becoming an increasingly prevalent vector for the dissemination of antibiotic resistances in Vibrio cholerae. SXT is a member of a larger family of elements, formerly defined as IncJ plasmids, that are self-transmissible by conjugation and integrate site-specifically...

  • Altered PPARγ expression inhibits myogenic differentiation in C2C12 skeletal muscle cells. Jaskirat Singh; Navin Verma; Sejal M. Kansagra; Bhusan N. Kate // Molecular & Cellular Biochemistry;Jan2007, Vol. 294 Issue 1, p163 

    Abstract??Peroxisome proliferator-activated receptor ? (PPAR?) is a member of the nuclear receptor superfamily known to regulate adipocyte differentiation. However, its role in skeletal muscle differentiation is not known. To investigate possible involvement of PPAR? in skeletal muscle...

  • 816. Rapid, Consistent and Scalable Production of Viral Vectors in Suspension Cells by Cotransfection of Viral Component Plasmid DNA or RNA. Brady, James; Shivakumar, Rama; Malehorn, Matthew; Feller, Stephanie; Allen, Cornell; Linhong Li; Chopas, Nicholas; Dzekunov, Sergey; Peshwa, Madhusudan V.; Liu, Linda N. // Molecular Therapy;Jun2006, Vol. 13, pS317 

    Viral vectors show promise as gene therapy treatments for a number of diseases. However, it has been difficult to develop a robust system for generating large volumes of high-titer viral vectors based on lentivirus, alphavirus and adeno-associated virus (AAV) that are needed for clinical...

  • 695. Low-Frequency Ultrasound Increases Non-Viral Lung Gene Transfer. Stefania Xenariou; Hai-Dong Liang; Griesenbach, Uta; Jie Zhu; Farley, Raymond; Somerton, Lucinda; Singh, Charanjit; Jeffery, Peter K.; Scheule, Ronald K.; Cheng, Seng H.; Geddes, Duncan M.; Blomley, Martin; Alton, Eric W. F. W. // Molecular Therapy;Jun2006, Vol. 13, pS269 

    We have previously shown that high-frequency (1 MHz) ultrasound (U/S) increases naked plasmid DNA (pDNA) gene transfer in the mouse lung and that this effect requires microbubbles (Optison) to be present in the formulation. Here, we assessed low-frequency (30–35 kHz) U/S, in an attempt to...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics