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Mechanisms of Evolution

Beyond Darwin and Neo-Darwinism

reference articles

»» STANFORD RESEARCHERS DEVELOP SYSTEM FOR FIELD TESTING MECHANISMS OF EVOLUTION »» HORIZONTAL GENE TRANSFER, GENOME INNOVATION AND EVOLUTION »» New Evidence For One-way Evolution »» MICROBIOLOGY: ON TYPE IV SECRETION »» Where 'Jumping Genes' Fear To Tread »» New Cellular Evolution Theory Rejects Darwinian Assumptions »» Mobile DNA in obligate intracellular bacteria »» Symbiosis: Teaming up in defence »» Horizontal gene transfer, genome innovation and evolution »» Metabolic maps and functions of the Plasmodium falciparum apicoplast »» Hatena : Search : Endosymbiosis »» Search results : endosymbiosis : Nature »» RE-EVALUATING PROKARYOTIC SPECIES »» STUDYING PLASMID HORIZONTAL TRANSFER IN SITU: A CRITICAL REVIEW »» MECHANISMS OF, AND BARRIERS TO, HORIZONTAL GENE TRANSFER BETWEEN BACTERIA

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Nature Reviews Microbiology - Reviews: "To what extent is the tree of life the best representation of the evolutionary history of microorganisms? Recent work has shown that, among sets of prokaryotic genomes in which most homologous genes show extremely low sequence divergence, gene content can vary enormously, implying that those genes that are variably present or absent are frequently horizontally transferred.
Traditionally, successful horizontal gene transfer was assumed to provide a selective advantage to either the host or the gene itself, but could horizontally transferred genes be neutral or nearly neutral? We suggest that for many prokaryotes, the boundaries between species are fuzzy, and therefore the principles of population genetics must be broadened so that they can be applied to higher taxonomic categories.

Tree-like binary schemes for taxonomic classification have an illustrious history in evolutionary biology, but they do not provide a complete representation of life's history, especially for prokaryotes. Some genes within an organism have tree-like histories that differ from the histories of other genes within the same organism, owing to horizontal gene transfer (HGT). Although all types of genes can be susceptible to horizontal transfer, different types of genes and groups of organisms vary in their propensity for HGT.
Phylogenetic analysis of a concatenation of genes with differing gene histories has the potential to create artifactual histories that reflect neither the history of the organism nor the history of the gene. Methods of phylogenetic reconstruction that do not insist on tree-like phylogenies but explicitly allow for reticulation events promise to yield a more realistic reconstruction of much of life's history.

Phylogenetic reconstruction methodology — and therefore the accurate detection of historical HGT events — can benefit from a better understanding of phylogenetic signal as it relates to rates of change of characters and taxonomic sampling.

The abundance and atypical composition of genes that are transient in prokaryotic genomes such as that of Escherichia coli lead one to wonder whether such genes (and horizontally transferred genes in general) are deleterious, selected for or neutral on transfer. Recent studies seem to indicate extensive gene swapping and few selective sweeps, arguing that many transferred genes might be nearly neutral in selective effect.
Quantitative methods for analysing the frequency and nature of HGT events in microbial communities are needed. Quantitative descriptions yield precise predictions that can be tested statistically, and will help to resolve disputes about the frequency and importance of HGT to microbial evolution by improving clarity of expression, as well as enforcing statistical decision criteria."

J. Peter Gogarten & Jeffrey P. Townsend about the authors HORIZONTAL GENE TRANSFER, GENOME INNOVATION AND EVOLUTION
Nature Reviews Microbiology 3, 679-687 (2005); doi:10.1038/nrmicro1204

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New Evidence For One-way Evolution

UCSD Biologists Find New Evidence For One-way Evolution: "Irreversible loss of complex traits, which result from the combined interaction of several genes, is an old and at times controversial scientific question. While the late evolutionary biologist Stephen Jay Gould popularized the hypothesis of irreversibility, known as Dollo's Law, studies that use current methods to reconstruct the evolution of complex traits often fail to support it. This is because it is often difficult to reconstruct characteristics of extinct ancestors with any certainty."

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MICROBIOLOGY: ON TYPE IV SECRETION: "Possibly the most familiar example of such an apparatus is the conjugation machinery, a multiprotein complex that facilitates the transfer of genetic material from one bacterial cell to another. In the natural environment, this form of horizontal gene transfer promotes genetic diversity and survival. "

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Where 'Jumping Genes' Fear To Tread

Where 'Jumping Genes' Fear To Tread: "Scientists from the University of Queensland report in the journal Genome Research that large segments of the human genome are conspicuously devoid of ubiquitous mobile DNA elements called transposons. The locations of these regions are highly conserved among mammalian species and are enriched in genes crucial for the regulation of developmental processes.

Transposons, often called "jumping genes," are DNA sequences that have the capacity to move from one chromosomal site to another. More than three million copies of transposons have accumulated in humans throughout the course of evolution and now comprise an estimated 45% of the total DNA content in the human genome.

These mobile genetic elements are scattered throughout the human genome -- separated, on average, by only 500 base pairs. But Dr. John Mattick's laboratory at the University of Queensland, Australia, identified long tracks of genomic segments (greater than 10 kilobases in length) that lack transposable elements. His team identified 860 such sequences in humans, 993 in mice, and 559 in opossums. They named these segments TFRs, or transposon-free regions.

"Strikingly," says Mattick, "many TFRs in the human genome occur in the same position in the mouse and opossum genomes, despite the fact that transposons entered each lineage independently, after each species diverged from a common ancestor. It appears that many TFRs are evolutionarily conserved features that existed prior to -- and have been largely maintained since -- the divergence of eutherian mammals and marsupials approximately 170 million years ago."

The opossum was chosen for inclusion in the analysis because it is a marsupial that has a similar load of transposable elements compared to mice and humans but is evolutionarily distant from the two species. In contrast, the genomes of chicken and fish, which diverged from humans more than 300 million years ago, do not have a significant density of transposons.

Given the strong evolutionary conservation of the TFRs, Mattick's group hypothesized that they are regions of significant biological importance. Upon further characterizing the TFRs, they discovered that many (85%) overlapped at least one annotated gene and that almost all (94%) overlapped at least one known RNA transcript. In addition, the TFRs were enriched in microRNAs, in genes that encode proteins with putative DNA-binding activity, and in genes that are involved in developmental processes. Another striking feature of TFRs was that they are associated with ultra-conserved regions, or genomic segments longer than 200 base pairs with 100% identity between human, mouse, and rat. All of these observations strongly support an important role for TFRs in critical biological processes.

"The majority of the TFRs lie outside of protein-coding sequences, so they presumably represent regions of regulatory information or RNA transcripts that cannot be disrupted. However, it's difficult to explain mechanistically the requirement of 10 or more kilobases of uninterrupted sequence in terms of the current paradigms of transcriptional regulation," explains Mattick. "It appears that TFRs might be the passive signatures of one or more poorly understood mechanisms of gene regulation that operate in higher organisms, suggesting a wider role for noncoding sequences than has hitherto been appreciated." "

External : Transposons part 1, transposons part 2 : Barbara McClintock and mobile genetic elements :

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New Cellular Evolution Theory Rejects Darwinian Assumptions

New Cellular Evolution Theory Rejects Darwinian Assumptions: "Life did not begin with one primordial cell. Instead, there were initially at least three simple types of loosely constructed cellular organizations. They swam in a pool of genes, evolving in a communal way that aided one another in bootstrapping into the three distinct types of cells by sharing their evolutionary inventions. The driving force in evolving cellular life on Earth, says Carl Woese, a microbiologist at the University of Illinois at Urbana-Champaign, has been horizontal gene transfer, in which the acquisition of alien cellular components, including genes and proteins, work to promote the evolution of recipient cellular entities. Woese presents his theory of cellular evolution, which challenges long-held traditions and beliefs of biologists, in the June 18 issue of the Proceedings of the National Academy of Sciences.

Cellular evolution, he argues, began in a communal environment in which the loosely organized cells took shape through extensive horizontal gene transfer. Such a transfer previously had been recognized as having a minor role in evolution, but the arrival of microbial genomics, Woese says, is shedding a more accurate light. Horizontal gene transfer, he argues, has the capacity to rework entire genomes. With simple primitive entities this process can "completely erase an organismal genealogical trace."
His theory challenges the longstanding Darwinian assumption known as the Doctrine of Common Descent – that all life on Earth has descended from one original primordial form. "

Original news release

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Mobile DNA in obligate intracellular bacteria

Search results : endosymbiosis : Nature: "7.Mobile DNA in obligate intracellular bacteria
Seth R. Bordenstein, William S. Reznikoff
SUMMARY: The small genomes of obligate intracellular bacteria are often presumed to be impervious to mobile DNA and the fluid genetic processes that drive diversification
CONTEXT: ...Moran, N. A. & Baumann, P. . Curr. Opin. Microbiol. 3, 270�275 (2000). Buchner, P. Endosymbiosis of Animals with Plant Microorganisms (Interscience Publishers, John Wiley...
Nature Reviews Microbiology 3, 688-699 (01 Sep 2005) Review
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Symbiosis: Teaming up in defence

Search results : endosymbiosis : Nature: "5.Symbiosis: Teaming up in defence
Susan Jones
CONTEXT: ...are renowned for secondary metabolite production, but this is the first example of an endosymbiosis involving a streptomycete. Prior to metamorphosis, larvae spin a cocoon,...
Nature Reviews Microbiology 3, 367-367 (01 May 2005) Highlights
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Horizontal gene transfer, genome innovation and evolution

Search results : endosymbiosis : Nature: "4.Horizontal gene transfer, genome innovation and evolution
J. Peter Gogarten, Jeffrey P. Townsend
SUMMARY: To what extent is the tree of life the best representation of the evolutionary history of microorganisms? Recent work has shown that, among sets
CONTEXT: cellular evolution, that is, the mitochondria and plastids, are the result of endosymbiosis. Throughout the decades, MUTUALISM and RETICULATION have often been...
Nature Reviews Microbiology 3, 679-687 (01 Sep 2005) Review
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Metabolic maps and functions of the Plasmodium falciparum apicoplast

Search results : endosymbiosis : Nature: "3.: Metabolic maps and functions of the Plasmodium falciparum apicoplast
Stuart A. Ralph, Giel G. van Dooren, Ross F. Waller, Michael J. Crawford, Martin J. Fraunholz, Bernardo J. Foth, Christopher J. Tonkin, David S. Roos, Geoffrey I. McFadden
SUMMARY: Discovery of a relict chloroplast (the apicoplast) in malarial parasites presented new opportunities for drug development. The apicoplast — although no longer photosynthetic —
CONTEXT: ...of the malaria parasite's distant photosynthetic ancestry. Plastids are derived from the endosymbiosis of cyanobacteria, and the apicoplast is no exception. Importantly,...
Nature Reviews Microbiology 2, 203-216 (01 Mar 2004) Review
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Hatena : Search : Endosymbiosis

Search results : endosymbiosis : Nature: "2.In brief
CONTEXT: ...I. Science 310, 287 (2005) This study describes the formative stages of a secondary endosymbiosis between a protist, here referred to as Hatena ('enigmatic' in Japanese),...
Nature Reviews Microbiology 3, 911-911 (01 Dec 2005)
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Search results : endosymbiosis : Nature

Search results : endosymbiosis : Nature: "
1. Genome watch: Fitting the niche by genomic adaptation
Nicholas Thomson, Stephen Bentley, Matthew Holden, Julian Parkhill
SUMMARY: Studying microbial genomics has shown that the genomes of bacteria are extremely dynamic in evolutionary terms. Many research groups have linked the adaptation of
CONTEXT: ...the authors to produce a hypothetical minimal set of genes that are necessary to sustain endosymbiosis. Curiously, the genome lacks several genes that are involved in...
Nature Reviews Microbiology 1, 92-93 (01 Nov 2003)
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Nature Reviews Microbiology - Perspectives: "There is no widely accepted concept of species for prokaryotes, and assignment of isolates to species is based on measures of phenotypic or genome similarity. The current methods for defining prokaryotic species are inadequate and incapable of keeping pace with the levels of diversity that are being uncovered in nature. Prokaryotic taxonomy is being influenced by advances in microbial population genetics, ecology and genomics, and by the ease with which sequence data can be obtained. Here, we review the classical approaches to prokaryotic species definition and discuss the current and future impact of multilocus nucleotide-sequence-based approaches to prokaryotic systematics. We also consider the potential, and difficulties, of assigning species status to biologically or ecologically meaningful sequence clusters."

Dirk Gevers, Frederick M. Cohan, Jeffrey G. Lawrence, Brian G. Spratt, Tom Coenye, Edward J. Feil, Erko Stackebrandt, Yves Van de Peer, Peter Vandamme, Fabiano L. Thompson & Jean Swings RE-EVALUATING PROKARYOTIC SPECIES Nature Reviews Microbiology 3, 733-739 (2005); doi:10.1038/nrmicro1236

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Nature Reviews Microbiology - Reviews: "This review deals with the prospective, experimental documentation of horizontal gene transfer (HGT) and its role in real-time, local adaptation. We have focused on plasmids and their function as an accessory and/or adaptive gene pool. Studies of the extent of HGT in natural environments have identified certain hot spots, and many of these involve biofilms. Biofilms are uniquely suited for HGT, as they sustain high bacterial density and metabolic activity, even in the harshest environments. Single-cell detection of donor, recipient and transconjugant bacteria in various natural environments, combined with individual-based mathematical models, has provided a new platform for HGT studies."

Søren J. Sørensen, Mark Bailey, Lars H. Hansen, Niels Kroer & Stefan Wuertz STUDYING PLASMID HORIZONTAL TRANSFER IN SITU: A CRITICAL REVIEW Nature Reviews Microbiology 3, 700-710 (2005); doi:10.1038/nrmicro1232

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Nature Reviews Microbiology - Reviews: "Bacteria evolve rapidly not only by mutation and rapid multiplication, but also by transfer of DNA, which can result in strains with beneficial mutations from more than one parent. Transformation involves the release of naked DNA followed by uptake and recombination. Homologous recombination and DNA-repair processes normally limit this to DNA from similar bacteria. However, if a gene moves onto a broad-host-range plasmid it might be able to spread without the need for recombination. There are barriers to both these processes but they reduce, rather than prevent, gene acquisition."

Christopher M. Thomas & Kaare M. Nielsen MECHANISMS OF, AND BARRIERS TO, HORIZONTAL GENE TRANSFER BETWEEN BACTERIA Nature Reviews Microbiology 3, 711-721 (2005); doi:10.1038/nrmicro1234

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Nature Reviews Microbiology - Reviews: "Horizontal genomics is a new field in prokaryotic biology that is focused on the analysis of DNA sequences in prokaryotic chromosomes that seem to have originated from other prokaryotes or eukaryotes. However, it is equally important to understand the agents that effect DNA movement: plasmids, bacteriophages and transposons. Although these agents occur in all prokaryotes, comprehensive genomics of the prokaryotic mobile gene pool or 'mobilome' lags behind other genomics initiatives owing to challenges that are distinct from cellular chromosomal analysis. Recent work shows promise of improved mobile genetic element (MGE) genomics and consequent opportunities to take advantage � and avoid the dangers � of these 'natural genetic engineers'. This review describes MGEs, their properties that are important in horizontal gene transfer, and current opportunities to advance MGE genomics.

Although MGEs are the main agents of horizontal gene transfer (HGT), relatively few have been sequenced and analysis of their genomic and phylogenetic properties lags behind that of organismal chromosomes. Specifically, the major databases do not curate plasmid and phage nucleic acid or protein sequences. Sequencing MGE genomes presents unique challenges because phages require suitable hosts for propagation and plasmids must be physically separated from each other and from the host chromosomal DNA. The relatively small size of MGEs (5−500 kb) and their varied GC content thwart current automated annotation algorithms."

Laura S. Frost, Raphael Leplae, Anne O. Summers & Ariane Toussaint MOBILE GENETIC ELEMENTS: THE AGENTS OF OPEN SOURCE EVOLUTION Nature Reviews Microbiology 3, 722-732 (2005); doi:10.1038/nrmicro1235

External : Transposons part 1, transposons part 2 : Barbara McClintock and mobile genetic elements :

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Nature Reviews Microbiology - Reviews: "Horizontal gene transfer is an important mechanism for the evolution of microbial genomes. Pathogenicity islands � mobile genetic elements that contribute to rapid changes in virulence potential � are known to have contributed to genome evolution by horizontal gene transfer in many bacterial pathogens. Increasing evidence indicates that equivalent elements in non-pathogenic species � genomic islands � are important in the evolution of these bacteria, influencing traits such as antibiotic resistance, symbiosis and fitness, and adaptation in general. This review discusses the recent lessons that have been learned from pathogenicity islands in pathogenic microorganisms and how they apply to the role of genomic islands in commensal, symbiotic and environmental bacteria.

Genomic islands (GEIs) are characterized by their large size (>10 kb), their frequent association with tRNA-encoding genes and a different G+C content compared with the rest of the chromosome. Many genomic islands are flanked by repeat structures and carry fragments of other mobile and accessory genetic elements, such as bacteriophages, plasmids and insertion sequence (IS) elements.

Some GEIs can excise themselves spontaneously from the chromosome and can be transferred to other suitable recipients. GEIs contribute to bacterial genome plasticity and, together with other mobile and accessory genetic elements, to the 'horizontal gene pool' of a given bacterial population.

A hypothetical 'life cycle' of GEIs includes the insertion of mobile genetic elements into the bacterial chromosome. Through rearrangements and consecutive insertion and deletion events, the organization and gene content of the original element becomes modified and can lose the features of mobile elements. Owing to the action of bacteriophage integrases that are encoded on genomic islands, these genetic elements can be deleted from the chromosome and, upon transfer into a suitable host, can be chromosomally inserted by site-specific recombination.

GEIs contribute to fitness and adaptation. GEIs typically provide a gain-of-function to the host bacterium. As GEIs promote the transfer of multi-gene families, entire phenotypes can be changed in a single-step gene-transfer event.

GEIs are expected to have a role in ecological niches where microbial cell numbers and diversity are high and/or in environments that are constantly changing. The GEIs identified so far are relevant in the context of pathogenicity, symbiosis, antibiotic resistance, xenobiotic degradation, and primary and secondary metabolism. It is expected that the functional diversity of GEIs is even greater than is currently known.

As GEIs are widely distributed in pathogenic, non-pathogenic and environmental microorganisms, they represent a paradigm rather than a paradox for microbial evolution, underlining the importance of horizontal gene transfer in this process."

Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jörg Hacker GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038/nrmicro884

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Nature Reviews Microbiology - Perspectives: "Evolutionary microbiology is a basic science that is increasingly forming the basis for new developments in public-health microbiology. Medical advances might depend on an understanding of the conditions that are required for the emergence and maintenance of human bacterial pathogens. An understanding of the evolutionary engineering rules that lead to virulence or drug resistance � specifically with bacteria in mind � are therefore important and are examined in this article."

Fernando Baquero FROM PIECES TO PATTERNS: EVOLUTIONARY ENGINEERING IN BACTERIAL Nature Reviews Microbiology 2, 510-518 (2004); doi:10.1038/nrmicro909 PATHOGENS

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Nature Reviews Microbiology - Reviews: "Bacterial genomes are increasingly viewed in terms of the integration of accessory and dispensable genetic elements into a conserved genomic core. This duality provides both the evolutionary stability that is required for the maintenance of essential functions and the flexibility that is needed for rapid exploitation of new niches. This review focuses on combining genome sequencing, microarray and multilocus sequence data to explore microevolutionary divergence in single species and genera.

Bacterial genomes are composed of essential 'core' genes, encoding functions relating to central metabolism and informational processing, and 'accessory' genes that commonly encode supplementary metabolic pathways and virulence factors. 'Foreign' genes in bacterial genomes can be identified by atypical base composition; these might have been imported from quite distant bacterial taxa.

Three main tools for examining the microevolution (evolution within species) of bacteria are complete genome sequencing, microarray analysis (which detects changes in gene content) and multi-locus sequencing of 'core' genes. These three approaches have advantages and disadvantages and are most powerfully used in combination.

Most bacterial populations consist of a limited number of widespread clonal complexes on the basis of sequence variation in a sample of core genes. These clonal complexes are generally robust with respect to gene choice and are meaningful biological units. These clusters might represent adaptations to specific microniches, and be set on independent evolutionary trajectories.

Despite high degrees of clonality, analysis of clonal diversification and phylogenetic approaches examining the relationships between clones both indicate that homologous recombination is an important evolutionary force in many bacterial populations. It is possible that sampling bias leads to an artificially high degree of clonality, but also that the selective origin of clones allows them to withstand the homogenizing effects of recombination.

Given the clonal structure of bacterial populations, comparative genomic analysis is most fruitfully carried out with reference to clonal assignments. Such an approach allows a consideration of likely ecological adaptations between isolates and a broad temporal perspective to microevolutionary studies."

Edward J. Feil SMALL CHANGE: KEEPING PACE WITH MICROEVOLUTION Nature Reviews Microbiology 2, 483-495 (2004); doi:10.1038/nrmicro904

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