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1.  Quantifying Homologous Replacement of Loci between Haloarchaeal Species 
Genome Biology and Evolution  2012;4(12):1223-1244.
In vitro studies of the haloarchaeal genus Haloferax have demonstrated their ability to frequently exchange DNA between species, whereas rates of homologous recombination estimated from natural populations in the genus Halorubrum are high enough to maintain random association of alleles between five loci. To quantify the effects of gene transfer and recombination of commonly held (relaxed core) genes during the evolution of the class Halobacteria (haloarchaea), we reconstructed the history of 21 genomes representing all major groups. Using a novel algorithm and a concatenated ribosomal protein phylogeny as a reference, we created a directed horizontal genetic transfer (HGT) network of contemporary and ancestral genomes. Gene order analysis revealed that 90% of testable HGTs were by direct homologous replacement, rather than nonhomologous integration followed by a loss. Network analysis revealed an inverse log-linear relationship between HGT frequency and ribosomal protein evolutionary distance that is maintained across the deepest divergences in Halobacteria. We use this mathematical relationship to estimate the total transfers and amino acid substitutions delivered by HGTs in each genome, providing a measure of chimerism. For the relaxed core genes of each genome, we conservatively estimate that 11–20% of their evolution occurred in other haloarchaea. Our findings are unexpected, because the transfer and homologous recombination of relaxed core genes between members of the class Halobacteria disrupts the coevolution of genes; however, the generation of new combinations of divergent but functionally related genes may lead to adaptive phenotypes not available through cumulative mutations and recombination within a single population.
doi:10.1093/gbe/evs098
PMCID: PMC3542582  PMID: 23160063
homologous recombination; horizontal gene transfer; lateral gene transfer; fitness landscape; populations; microbial evolution
2.  Reconstructed Ancestral Myo-Inositol-3-Phosphate Synthases Indicate That Ancestors of the Thermococcales and Thermotoga Species Were More Thermophilic than Their Descendants 
PLoS ONE  2013;8(12):e84300.
The bacterial genomes of Thermotoga species show evidence of significant interdomain horizontal gene transfer from the Archaea. Members of this genus acquired many genes from the Thermococcales, which grow at higher temperatures than Thermotoga species. In order to study the functional history of an interdomain horizontally acquired gene we used ancestral sequence reconstruction to examine the thermal characteristics of reconstructed ancestral proteins of the Thermotoga lineage and its archaeal donors. Several ancestral sequence reconstruction methods were used to determine the possible sequences of the ancestral Thermotoga and Archaea myo-inositol-3-phosphate synthase (MIPS). These sequences were predicted to be more thermostable than the extant proteins using an established sequence composition method. We verified these computational predictions by measuring the activities and thermostabilities of purified proteins from the Thermotoga and the Thermococcales species, and eight ancestral reconstructed proteins. We found that the ancestral proteins from both the archaeal donor and the Thermotoga most recent common ancestor recipient were more thermostable than their descendants. We show that there is a correlation between the thermostability of MIPS protein and the optimal growth temperature (OGT) of its host, which suggests that the OGT of the ancestors of these species of Archaea and the Thermotoga grew at higher OGTs than their descendants.
doi:10.1371/journal.pone.0084300
PMCID: PMC3877268  PMID: 24391933
3.  Vitamin B12 Synthesis and Salvage Pathways Were Acquired by Horizontal Gene Transfer to the Thermotogales 
Genome Biology and Evolution  2012;4(8):842-851.
The availability of genome sequences of Thermotogales species from across the order allows an examination of the evolutionary origins of phenotypic characteristics in this lineage. Several studies have shown that the Thermotogales have acquired large numbers of genes from distantly related lineages, particularly Firmicutes and Archaea. Here, we report the finding that some Thermotogales acquired the ability to synthesize vitamin B12 by acquiring the requisite genes from these distant lineages. Thermosipho species, uniquely among the Thermotogales, contain genes that encode the means to synthesize vitamin B12 de novo from glutamate. These genes are split into two gene clusters: the corrinoid synthesis gene cluster, that is unique to the Thermosipho and the cobinamide salvage gene cluster. The corrinoid synthesis cluster was acquired from the Firmicutes lineage, whereas the salvage pathway is an amalgam of bacteria- and archaea-derived proteins. The cobinamide salvage gene cluster has a patchy distribution among Thermotogales species, and ancestral state reconstruction suggests that this pathway was present in the common Thermotogales ancestor. We show that Thermosipho africanus can grow in the absence of vitamin B12, so its de novo pathway is functional. We detected vitamin B12 in the extracts of T. africanus cells to verify the synthetic pathway. Genes in T. africanus with apparent B12 riboswitches were found to be down-regulated in the presence of vitamin B12 consistent with their roles in B12 synthesis and cobinamide salvage.
doi:10.1093/gbe/evs057
PMCID: PMC3509894  PMID: 22798452
cobalamin; cobinamide; Thermotogales; vitamin B12; horizontal gene transfer
4.  Ancient origin of the divergent forms of leucyl-tRNA synthetases in the Halobacteriales 
Background
Horizontal gene transfer (HGT) has greatly impacted the genealogical history of many lineages, particularly for prokaryotes, with genes frequently moving in and out of a line of descent. Many genes that were acquired by a lineage in the past likely originated from ancestral relatives that have since gone extinct. During the course of evolution, HGT has played an essential role in the origin and dissemination of genetic and metabolic novelty.
Results
Three divergent forms of leucyl-tRNA synthetase (LeuRS) exist in the archaeal order Halobacteriales, commonly known as haloarchaea. Few haloarchaeal genomes have the typical archaeal form of this enzyme and phylogenetic analysis indicates it clusters within the Euryarchaeota as expected. The majority of sequenced halobacterial genomes possess a bacterial form of LeuRS. Phylogenetic reconstruction puts this larger group of haloarchaea at the base of the bacterial domain. The most parsimonious explanation is that an ancient transfer of LeuRS took place from an organism related to the ancestor of the bacterial domain to the haloarchaea. The bacterial form of LeuRS further underwent gene duplications and/or gene transfers within the haloarchaea, with some genomes possessing two distinct types of bacterial LeuRS. The cognate tRNALeu also reveals two distinct clusters for the haloarchaea; however, these tRNALeu clusters do not coincide with the groupings found in the LeuRS tree, revealing that LeuRS evolved independently of its cognate tRNA.
Conclusions
The study of leucyl-tRNA synthetase in haloarchaea illustrates the importance of gene transfer originating in lineages that went extinct since the transfer occurred. The haloarchaeal LeuRS and tRNALeu did not co-evolve.
doi:10.1186/1471-2148-12-85
PMCID: PMC3436685  PMID: 22694720
5.  Quartet decomposition server: a platform for analyzing phylogenetic trees 
BMC Bioinformatics  2012;13:123.
Background
The frequent exchange of genetic material among prokaryotes means that extracting a majority or plurality phylogenetic signal from many gene families, and the identification of gene families that are in significant conflict with the plurality signal is a frequent task in comparative genomics, and especially in phylogenomic analyses. Decomposition of gene trees into embedded quartets (unrooted trees each with four taxa) is a convenient and statistically powerful technique to address this challenging problem. This approach was shown to be useful in several studies of completely sequenced microbial genomes.
Results
We present here a web server that takes a collection of gene phylogenies, decomposes them into quartets, generates a Quartet Spectrum, and draws a split network. Users are also provided with various data download options for further analyses. Each gene phylogeny is to be represented by an assessment of phylogenetic information content, such as sets of trees reconstructed from bootstrap replicates or sampled from a posterior distribution. The Quartet Decomposition server is accessible at http://quartets.uga.edu.
Conclusions
The Quartet Decomposition server presented here provides a convenient means to perform Quartet Decomposition analyses and will empower users to find statistically supported phylogenetic conflicts.
doi:10.1186/1471-2105-13-123
PMCID: PMC3447714  PMID: 22676320
6.  Structural stability and endonuclease activity of a PI-SceI GFP-fusion protein 
Homing endonucleases are site-specific and rare cutting endonucleases often encoded by intron or intein containing genes. They lead to the rapid spread of the genetic element that hosts them by a process termed 'homing'; and ultimately the allele containing the element will be fixed in the population.
PI-SceI, an endonuclease encoded as a protein insert or intein within the yeast V-ATPase catalytic subunit encoding gene (vma1), is among the best characterized homing endonucleases. The structures of the Sce VMA1 intein and of the intein bound to its target site are known. Extensive biochemical studies performed on the PI-SceI enzyme provide information useful to recognize critical amino acids involved in self-splicing and endonuclease functions of the protein. Here we describe an insertion of the Green Fluorescence Protein (GFP) into a loop which is located between the endonuclease and splicing domains of the Sce VMA1 intein. The GFP is functional and the additional GFP domain does not prevent intein excision and endonuclease activity. However, the endonuclease activity of the newly engineered protein was different from the wild-type protein in that it required the presence of Mn2+ and not Mg2+ metal cations for activity.
PMCID: PMC1802021  PMID: 17389927
Homing endonuclease; intein; GFP-fusion protein; PI-SceI; Sce VMA
7.  Biased gene transfer and its implications for the concept of lineage 
Biology Direct  2011;6:47.
Background
In the presence of horizontal gene transfer (HGT), the concepts of lineage and genealogy in the microbial world become more ambiguous because chimeric genomes trace their ancestry from a myriad of sources, both living and extinct.
Results
We present the evolutionary histories of three aminoacyl-tRNA synthetases (aaRS) to illustrate that the concept of organismal lineage in the prokaryotic world is defined by both vertical inheritance and reticulations due to HGT. The acquisition of a novel gene from a distantly related taxon can be considered as a shared derived character that demarcates a group of organisms, as in the case of the spirochaete Phenylalanyl-tRNA synthetase (PheRS). On the other hand, when organisms transfer genetic material with their close kin, the similarity and therefore relatedness observed among them is essentially shaped by gene transfer. Studying the distribution patterns of divergent genes with identical functions, referred to as homeoalleles, can reveal preferences for transfer partners. We describe the very ancient origin and the distribution of the archaeal homeoalleles for Threonyl-tRNA synthetases (ThrRS) and Seryl-tRNA synthetases (SerRS).
Conclusions
Patterns created through biased HGT can be undistinguishable from those created through shared organismal ancestry. A re-evaluation of the definition of lineage is necessary to reflect genetic relatedness due to both HGT and vertical inheritance. In most instances, HGT bias will maintain and strengthen similarity within groups. Only in cases where HGT bias is due to other factors, such as shared ecological niche, do patterns emerge from gene phylogenies that are in conflict with those reflecting shared organismal ancestry.
Reviewers
This article was reviewed by W. Ford Doolittle, François-Joseph Lapointe, and Frederic Bouchard.
doi:10.1186/1745-6150-6-47
PMCID: PMC3191353  PMID: 21943000
8.  A Rooted Net of Life 
Biology Direct  2011;6:45.
Abstract
Phylogenetic reconstruction using DNA and protein sequences has allowed the reconstruction of evolutionary histories encompassing all life. We present and discuss a means to incorporate much of this rich narrative into a single model that acknowledges the discrete evolutionary units that constitute the organism. Briefly, this Rooted Net of Life genome phylogeny is constructed around an initial, well resolved and rooted tree scaffold inferred from a supermatrix of combined ribosomal genes. Extant sampled ribosomes form the leaves of the tree scaffold. These leaves, but not necessarily the deeper parts of the scaffold, can be considered to represent a genome or pan-genome, and to be associated with members of other gene families within that sequenced (pan)genome. Unrooted phylogenies of gene families containing four or more members are reconstructed and superimposed over the scaffold. Initially, reticulations are formed where incongruities between topologies exist. Given sufficient evidence, edges may then be differentiated as those representing vertical lines of inheritance within lineages and those representing horizontal genetic transfers or endosymbioses between lineages.
Reviewers
W. Ford Doolittle, Eric Bapteste and Robert Beiko.
doi:10.1186/1745-6150-6-45
PMCID: PMC3189188  PMID: 21936906
9.  Reassessment of the Lineage Fusion Hypothesis for the Origin of Double Membrane Bacteria 
PLoS ONE  2011;6(8):e23774.
In 2009, James Lake introduced a new hypothesis in which reticulate phylogeny reconstruction is used to elucidate the origin of Gram-negative bacteria (Nature 460: 967–971). The presented data supported the Gram-negative bacteria originating from an ancient endosymbiosis between the Actinobacteria and Clostridia. His conclusion was based on a presence-absence analysis of protein families that divided all prokaryotes into five groups: Actinobacteria, Double Membrane bacteria (DM), Clostridia, Archaea and Bacilli. Of these five groups, the DM are by far the largest and most diverse group compared to the other groupings. While the fusion hypothesis for the origin of double membrane bacteria is enticing, we show that the signal supporting an ancient symbiosis is lost when the DM group is broken down into smaller subgroups. We conclude that the signal detected in James Lake's analysis in part results from a systematic artifact due to group size and diversity combined with low levels of horizontal gene transfer.
doi:10.1371/journal.pone.0023774
PMCID: PMC3158100  PMID: 21876769
10.  Filling the gaps in the genomic landscape 
Genome Biology  2010;11(2):103.
Sequencing of genomes from many different bacterial and archaeal groups is broadening the picture of the prokaryotic pan-genome.
A new initiative provides comparative genomicists with a more complete picture of genome diversity. Here we discuss the improved sampling strategy.
doi:10.1186/gb-2010-11-2-103
PMCID: PMC2872866  PMID: 20210981
11.  Complex Evolutionary History of the Aeromonas veronii Group Revealed by Host Interaction and DNA Sequence Data 
PLoS ONE  2011;6(2):e16751.
Aeromonas veronii biovar sobria, Aeromonas veronii biovar veronii, and Aeromonas allosaccharophila are a closely related group of organisms, the Aeromonas veronii Group, that inhabit a wide range of host animals as a symbiont or pathogen. In this study, the ability of various strains to colonize the medicinal leech as a model for beneficial symbiosis and to kill wax worm larvae as a model for virulence was determined. Isolates cultured from the leech out-competed other strains in the leech model, while most strains were virulent in the wax worms. Three housekeeping genes, recA, dnaJ and gyrB, the gene encoding chitinase, chiA, and four loci associated with the type three secretion system, ascV, ascFG, aexT, and aexU were sequenced. The phylogenetic reconstruction failed to produce one consensus tree that was compatible with most of the individual genes. The Approximately Unbiased test and the Genetic Algorithm for Recombination Detection both provided further support for differing evolutionary histories among this group of genes. Two contrasting tests detected recombination within aexU, ascFG, ascV, dnaJ, and gyrB but not in aexT or chiA. Quartet decomposition analysis indicated a complex recent evolutionary history for these strains with a high frequency of horizontal gene transfer between several but not among all strains. In this study we demonstrate that at least for some strains, horizontal gene transfer occurs at a sufficient frequency to blur the signal from vertically inherited genes, despite strains being adapted to distinct niches. Simply increasing the number of genes included in the analysis is unlikely to overcome this challenge in organisms that occupy multiple niches and can exchange DNA between strains specialized to different niches. Instead, the detection of genes critical in the adaptation to specific niches may help to reveal the physiological specialization of these strains.
doi:10.1371/journal.pone.0016751
PMCID: PMC3040217  PMID: 21359176
12.  Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life 
Horizontal gene transfer (HGT) is often considered to be a source of error in phylogenetic reconstruction, causing individual gene trees within an organismal lineage to be incongruent, obfuscating the ‘true’ evolutionary history. However, when identified as such, HGTs between divergent organismal lineages are useful, phylogenetically informative characters that can provide insight into evolutionary history. Here, we discuss several distinct HGT events involving all three domains of life, illustrating the selective advantages that can be conveyed via HGT, and the utility of HGT in aiding phylogenetic reconstruction and in dating the relative sequence of speciation events. We also discuss the role of HGT from extinct lineages, and its impact on our understanding of the evolution of life on Earth. Organismal phylogeny needs to incorporate reticulations; a simple tree does not provide an accurate depiction of the processes that have shaped life's history.
doi:10.1098/rstb.2009.0033
PMCID: PMC2873001  PMID: 19571243
horizontal gene transfer; chlamydiae; cyanobacteria; acetoclastic methanogenesis; pyrrolysine; extinct lineages
13.  Inferring the Ancient History of the Translation Machinery and Genetic Code via Recapitulation of Ribosomal Subunit Assembly Orders 
PLoS ONE  2010;5(3):e9437.
Universally conserved positions in ribosomal proteins have significant biases in amino acid usage, likely indicating the expansion of the genetic code at the time leading up to the most recent common ancestor(s) (MRCA). Here, we apply this principle to the evolutionary history of the ribosome before the MRCA. It has been proposed that the experimentally determined order of assembly for ribosomal subunits recapitulates their evolutionary chronology. Given this model, we produce a probabilistic evolutionary ordering of the universally conserved small subunit (SSU) and large subunit (LSU) ribosomal proteins. Optimizing the relative ordering of SSU and LSU evolutionary chronologies with respect to minimizing differences in amino acid usage bias, we find strong compositional evidence for a more ancient origin for early LSU proteins. Furthermore, we find that this ordering produces several trends in specific amino acid usages compatible with models of genetic code evolution.
doi:10.1371/journal.pone.0009437
PMCID: PMC2830423  PMID: 20208990
14.  Trees in the Web of Life 
Journal of Biology  2009;8(6):54.
Reconstructing the 'Tree of Life' is complicated by extensive horizontal gene transfer between diverse groups of organisms. While numerous conceptual and technical obstacles remain, a report in this issue of Journal of Biology from Koonin and colleagues on the largest-scale prokaryotic genomic reconstruction yet attempted shows that such a tree is discernible, although its branches cannot be traced.
doi:10.1186/jbiol160
PMCID: PMC2737374  PMID: 19664165
15.  Conservation of intron and intein insertion sites: implications for life histories of parasitic genetic elements 
Background
Inteins and introns are genetic elements that are removed from proteins and RNA after translation or transcription, respectively. Previous studies have suggested that these genetic elements are found in conserved parts of the host protein. To our knowledge this type of analysis has not been done for group II introns residing within a gene. Here we provide quantitative statistical support from an analyses of proteins that host inteins, group I introns, group II introns and spliceosomal introns across all three domains of life.
Results
To determine whether or not inteins, group I, group II, and spliceosomal introns are found preferentially in conserved regions of their respective host protein, conservation profiles were generated and intein and intron positions were mapped to the profiles. Fisher's combined probability test was used to determine the significance of the distribution of insertion sites across the conservation profile for each protein. For a subset of studied proteins, the conservation profile and insertion positions were mapped to protein structures to determine if the insertion sites correlate to regions of functional activity. All inteins and most group I introns were found to be preferentially located within conserved regions; in contrast, a bacterial intein-like protein, group II and spliceosomal introns did not show a preference for conserved sites.
Conclusions
These findings demonstrate that inteins and group I introns are found preferentially in conserved regions of their respective host proteins. Homing endonucleases are often located within inteins and group I introns and these may facilitate mobility to conserved regions. Insertion at these conserved positions decreases the chance of elimination, and slows deletion of the elements, since removal of the elements has to be precise as not to disrupt the function of the protein. Furthermore, functional constrains on the targeted site make it more difficult for hosts to evolve immunity to the homing endonuclease. Therefore, these elements will better survive and propagate as molecular parasites in conserved sites. In contrast, spliceosomal introns and group II introns do not show significant preference for conserved sites and appear to have adopted a different strategy to evade loss.
doi:10.1186/1471-2148-9-303
PMCID: PMC2814812  PMID: 20043855
16.  Prokaryotic evolution and the tree of life are two different things 
Biology Direct  2009;4:34.
Background
The concept of a tree of life is prevalent in the evolutionary literature. It stems from attempting to obtain a grand unified natural system that reflects a recurrent process of species and lineage splittings for all forms of life. Traditionally, the discipline of systematics operates in a similar hierarchy of bifurcating (sometimes multifurcating) categories. The assumption of a universal tree of life hinges upon the process of evolution being tree-like throughout all forms of life and all of biological time. In multicellular eukaryotes, the molecular mechanisms and species-level population genetics of variation do indeed mainly cause a tree-like structure over time. In prokaryotes, they do not. Prokaryotic evolution and the tree of life are two different things, and we need to treat them as such, rather than extrapolating from macroscopic life to prokaryotes. In the following we will consider this circumstance from philosophical, scientific, and epistemological perspectives, surmising that phylogeny opted for a single model as a holdover from the Modern Synthesis of evolution.
Results
It was far easier to envision and defend the concept of a universal tree of life before we had data from genomes. But the belief that prokaryotes are related by such a tree has now become stronger than the data to support it. The monistic concept of a single universal tree of life appears, in the face of genome data, increasingly obsolete. This traditional model to describe evolution is no longer the most scientifically productive position to hold, because of the plurality of evolutionary patterns and mechanisms involved. Forcing a single bifurcating scheme onto prokaryotic evolution disregards the non-tree-like nature of natural variation among prokaryotes and accounts for only a minority of observations from genomes.
Conclusion
Prokaryotic evolution and the tree of life are two different things. Hence we will briefly set out alternative models to the tree of life to study their evolution. Ultimately, the plurality of evolutionary patterns and mechanisms involved, such as the discontinuity of the process of evolution across the prokaryote-eukaryote divide, summons forth a pluralistic approach to studying evolution.
Reviewers
This article was reviewed by Ford Doolittle, John Logsdon and Nicolas Galtier.
doi:10.1186/1745-6150-4-34
PMCID: PMC2761302  PMID: 19788731
17.  Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus 
Prochlorococcus is a genus of marine cyanobacteria characterized by small cell and genome size, an evolutionary trend toward low GC content, the possession of chlorophyll b, and the absence of phycobilisomes. Whereas many shared derived characters define Prochlorococcus as a clade, many genome-based analyses recover them as paraphyletic, with some low-light adapted Prochlorococcus spp. grouping with marine Synechococcus. Here, we use 18 Prochlorococcus and marine Synechococcus genomes to analyze gene flow within and between these taxa. We introduce embedded quartet scatter plots as a tool to screen for genes whose phylogeny agrees or conflicts with the plurality phylogenetic signal, with accepted taxonomy and naming, with GC content, and with the ecological adaptation to high and low light intensities. We find that most gene families support high-light adapted Prochlorococcus spp. as a monophyletic clade and low-light adapted Prochlorococcus sp. as a paraphyletic group. But we also detect 16 gene families that were transferred between high-light adapted and low-light adapted Prochlorococcus sp. and 495 gene families, including 19 ribosomal proteins, that do not cluster designated Prochlorococcus and Synechococcus strains in the expected manner. To explain the observed data, we propose that frequent gene transfer between marine Synechococcus spp. and low-light adapted Prochlorococcus spp. has created a “highway of gene sharing” (Beiko RG, Harlow TJ, Ragan MA. 2005. Highways of gene sharing in prokaryotes. Proc Natl Acad Sci USA. 102:14332–14337) that tends to erode genus boundaries without erasing the Prochlorococcus-specific ecological adaptations.
doi:10.1093/gbe/evp032
PMCID: PMC2817427  PMID: 20333202
marine cyanobacteria; horizontal gene transfer; introgression; quartet decomposition; supertree; genome evolution
18.  Concerted gene recruitment in early plant evolution 
Genome Biology  2008;9(7):R109.
Analyses of the red algal Cyanidioschyzon genome identified 37 genes that were acquired from non-organellar sources prior to the split of red algae and green plants.
Background
Horizontal gene transfer occurs frequently in prokaryotes and unicellular eukaryotes. Anciently acquired genes, if retained among descendants, might significantly affect the long-term evolution of the recipient lineage. However, no systematic studies on the scope of anciently acquired genes and their impact on macroevolution are currently available in eukaryotes.
Results
Analyses of the genome of the red alga Cyanidioschyzon identified 37 genes that were acquired from non-organellar sources prior to the split of red algae and green plants. Ten of these genes are rarely found in cyanobacteria or have additional plastid-derived homologs in plants. These genes most likely provided new functions, often essential for plant growth and development, to the ancestral plant. Many remaining genes may represent replacements of endogenous homologs with a similar function. Furthermore, over 78% of the anciently acquired genes are related to the biogenesis and functionality of plastids, the defining character of plants.
Conclusion
Our data suggest that, although ancient horizontal gene transfer events did occur in eukaryotic evolution, the number of acquired genes does not predict the role of horizontal gene transfer in the adaptation of the recipient organism. Our data also show that multiple independently acquired genes are able to generate and optimize key evolutionary novelties in major eukaryotic groups. In light of these findings, we propose and discuss a general mechanism of horizontal gene transfer in the macroevolution of eukaryotes.
doi:10.1186/gb-2008-9-7-r109
PMCID: PMC2530860  PMID: 18611267
19.  Evolution of Acetoclastic Methanogenesis in Methanosarcina via Horizontal Gene Transfer from Cellulolytic Clostridia▿ †  
Journal of Bacteriology  2007;190(3):1124-1127.
Phylogenetic analysis confirmed that two genes required for acetoclastic methanogenesis, ackA and pta, were horizontally transferred to the ancestor of Methanosarcina from a derived cellulolytic organism in the class Clostridia. This event likely occurred within the last 475 million years, causing profound changes in planetary methane biogeochemistry.
doi:10.1128/JB.01382-07
PMCID: PMC2223567  PMID: 18055595
20.  Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales 
Background
The mal genes that encode maltose transporters have undergone extensive lateral transfer among ancestors of the archaea Thermococcus litoralis and Pyrococcus furiosus. Bacterial hyperthermophiles of the order Thermotogales live among these archaea and so may have shared in these transfers. The genome sequence of Thermotoga maritima bears evidence of extensive acquisition of archaeal genes, so its ancestors clearly had the capacity to do so. We examined deep phylogenetic relationships among the mal genes of these hyperthermophiles and their close relatives to look for evidence of shared ancestry.
Results
We demonstrate that the two maltose ATP binding cassette (ABC) transporter operons now found in Tc. litoralis and P. furiosus (termed mal and mdx genes, respectively) are not closely related to one another. The Tc. litoralis and P. furiosus mal genes are most closely related to bacterial mal genes while their respective mdx genes are archaeal. The genes of the two mal operons in Tt. maritima are not related to genes in either of these archaeal operons. They are highly similar to one another and belong to a phylogenetic lineage that includes mal genes from the enteric bacteria. A unique domain of the enteric MalF membrane spanning proteins found also in these Thermotogales MalF homologs supports their relatively close relationship with these enteric proteins. Analyses of genome sequence data from other Thermotogales species, Fervidobacterium nodosum, Thermosipho melanesiensis, Thermotoga petrophila, Thermotoga lettingae, and Thermotoga neapolitana, revealed a third apparent mal operon, absent from the published genome sequence of Tt. maritima strain MSB8. This third operon, mal3, is more closely related to the Thermococcales' bacteria-derived mal genes than are mal1 and mal2. F. nodosum, Ts. melanesiensis, and Tt. lettingae have only one of the mal1-mal2 paralogs. The mal2 operon from an unknown species of Thermotoga appears to have been horizontally acquired by a Thermotoga species that had only mal1.
Conclusion
These data demonstrate that the Tc. litoralis and P. furiosus mdx maltodextrin transporter operons arose in the Archaea while their mal maltose transporter operons arose in a bacterial lineage, but not the same lineage as the two maltose transporter operons found in the published Tt. maritima genome sequence. These Tt. maritima maltose transporters are phylogenetically and structurally similar to those found in enteric bacteria and the mal2 operon was horizontally transferred within the Thermotoga lineage. Other Thermotogales species have a third mal operon that is more closely related to the bacterial Thermococcales mal operons, but the data do not support a recent horizontal sharing of that operon between these groups.
doi:10.1186/1471-2148-8-7
PMCID: PMC2246101  PMID: 18197971
21.  BranchClust: a phylogenetic algorithm for selecting gene families 
BMC Bioinformatics  2007;8:120.
Background
Automated methods for assembling families of orthologous genes include those based on sequence similarity scores and those based on phylogenetic approaches. The first are easy to automate but usually they do not distinguish between paralogs and orthologs or have restriction on the number of taxa. Phylogenetic methods often are based on reconciliation of a gene tree with a known rooted species tree; a limitation of this approach, especially in case of prokaryotes, is that the species tree is often unknown, and that from the analyses of single gene families the branching order between related organisms frequently is unresolved.
Results
Here we describe an algorithm for the automated selection of orthologous genes that recognizes orthologous genes from different species in a phylogenetic tree for any number of taxa. The algorithm is capable of distinguishing complete (containing all taxa) and incomplete (not containing all taxa) families and recognizes in- and outparalogs. The BranchClust algorithm is implemented in Perl with the use of the BioPerl module for parsing trees and is freely available at .
Conclusion
BranchClust outperforms the Reciprocal Best Blast hit method in selecting more sets of putatively orthologous genes. In the test cases examined, the correctness of the selected families and of the identified in- and outparalogs was confirmed by inspection of the pertinent phylogenetic trees.
doi:10.1186/1471-2105-8-120
PMCID: PMC1853112  PMID: 17425803
22.  The power of phylogenetic approaches to detect horizontally transferred genes 
Background
Horizontal gene transfer plays an important role in evolution because it sometimes allows recipient lineages to adapt to new ecological niches. High genes transfer frequencies were inferred for prokaryotic and early eukaryotic evolution. Does horizontal gene transfer also impact phylogenetic reconstruction of the evolutionary history of genomes and organisms? The answer to this question depends at least in part on the actual gene transfer frequencies and on the ability to weed out transferred genes from further analyses. Are the detected transfers mainly false positives, or are they the tip of an iceberg of many transfer events most of which go undetected by current methods?
Results
Phylogenetic detection methods appear to be the method of choice to infer gene transfers, especially for ancient transfers and those followed by orthologous replacement. Here we explore how well some of these methods perform using in silico transfers between the terminal branches of a gamma proteobacterial, genome based phylogeny. For the experiments performed here on average the AU test at a 5% significance level detects 90.3% of the transfers and 91% of the exchanges as significant. Using the Robinson-Foulds distance only 57.7% of the exchanges and 60% of the donations were identified as significant. Analyses using bipartition spectra appeared most successful in our test case. The power of detection was on average 97% using a 70% cut-off and 94.2% with 90% cut-off for identifying conflicting bipartitions, while the rate of false positives was below 4.2% and 2.1% for the two cut-offs, respectively. For all methods the detection rates improved when more intervening branches separated donor and recipient.
Conclusion
Rates of detected transfers should not be mistaken for the actual transfer rates; most analyses of gene transfers remain anecdotal. The method and significance level to identify potential gene transfer events represent a trade-off between the frequency of erroneous identification (false positives) and the power to detect actual transfer events.
doi:10.1186/1471-2148-7-45
PMCID: PMC1847511  PMID: 17376230
23.  Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements 
Self splicing introns and inteins that rely on a homing endonuclease for propagation are parasitic genetic elements. Their life-cycle and evolutionary fate has been described through the homing cycle. According to this model the homing endonuclease is selected for function only during the spreading phase of the parasite. This phase ends when the parasitic element is fixed in the population. Upon fixation the homing endonuclease is no longer under selection, and its activity is lost through random processes. Recent analyses of these parasitic elements with functional homing endonucleases suggest that this model in its most simple form is not always applicable. Apparently, functioning homing endonuclease can persist over long evolutionary times in populations and species that are thought to be asexual or nearly asexual. Here we review these recent findings and discuss their implications. Reasons for the long-term persistence of a functional homing endonuclease include: More recombination (sexual and as a result of gene transfer) than previously assumed for these organisms; complex population structures that prevent the element from being fixed; a balance between active spreading of the homing endonuclease and a decrease in fitness caused by the parasite in the host organism; or a function of the homing endonuclease that increases the fitness of the host organism and results in purifying selection for the homing endonuclease activity, even after fixation in a local population. In the future, more detailed studies of the population dynamics of the activity and regulation of homing endonucleases are needed to decide between these possibilities, and to determine their relative contributions to the long term survival of parasitic genes within a population. Two outstanding publications on the amoeba Naegleria group I intron (Wikmark et al. BMC Evol Biol 2006, 6:39) and the PRP8 inteins in ascomycetes (Butler et al.BMC Evol Biol 2006, 6:42) provide important stepping stones towards integrated studies on how these parasitic elements evolve through time together with, or despite, their hosts.
doi:10.1186/1471-2148-6-94
PMCID: PMC1654191  PMID: 17101053
24.  Evolutionary and Diagnostic Implications of Intragenomic Heterogeneity in the 16S rRNA Gene in Aeromonas Strains 
Journal of Bacteriology  2005;187(18):6561-6564.
Sequencing 16S rRNA genes (SSU) cloned from Aeromonas strains revealed that strains contained up to six copies differing by ≤1.5%. The SSU copies from Aeromonas veronii LMG13695 clustered with sequences from four Aeromonas species. These results demonstrate intragenomic heterogeneity of SSU and suggest caution when using SSU to identify aeromonads.
doi:10.1128/JB.187.18.6561-6564.2005
PMCID: PMC1236645  PMID: 16159790
25.  PentaPlot: A software tool for the illustration of genome mosaicism 
BMC Bioinformatics  2005;6:139.
Background
Dekapentagonal maps depict the phylogenetic relationships of five genomes in a visually appealing diagram and can be viewed as an alternative to a single evolutionary consensus tree. In particular, the generated maps focus attention on those gene families that significantly deviate from the consensus or plurality phylogeny. PentaPlot is a software tool that computes such dekapentagonal maps given an appropriate probability support matrix.
Results
The visualization with dekapentagonal maps critically depends on the optimal layout of unrooted tree topologies representing different evolutionary relationships among five organisms along the vertices of the dekapentagon. This is a difficult optimization problem given the large number of possible layouts. At its core our tool utilizes a genetic algorithm with demes and a local search strategy to search for the optimal layout. The hybrid genetic algorithm performs satisfactorily even in those cases where the chosen genomes are so divergent that little phylogenetic information has survived in the individual gene families.
Conclusion
PentaPlot is being made publicly available as an open source project at .
doi:10.1186/1471-2105-6-139
PMCID: PMC1177926  PMID: 15938752

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