Biased gene transfer and its implications for the concept of lineage

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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).</p> <p>Conclusions</p> <p>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.</p> <p>Reviewers</p> <p>This article was reviewed by W. Ford Doolittle, François-Joseph Lapointe, and Frederic Bouchard.</p

Trees in the Web of Life

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

Inferring the Ancient History of the Translation Machinery and Genetic Code via Recapitulation of Ribosomal Subunit Assembly Orders

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

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\u27s 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

Unsupervised Learning in Detection of Gene Transfer

The tree representation as a model for organismal evolution has been in use since before Darwin. However, with the recent unprecedented access to biomolecular data, it has been discovered that, especially in the microbial world, individual genes making up the genome of an organism give rise to different and sometimes conflicting evolutionary tree topologies. This discovery calls into question the notion of a single evolutionary tree for an organism and gives rise to the notion of an evolutionary consensus tree based on the evolutionary patterns of the majority of genes in a genome embedded in a network of gene histories. Here, we discuss an approach to the analysis of genomic data of multiple genomes using bipartition spectral analysis and unsupervised learning. An interesting observation is that genes within genomes that have evolutionary tree topologies, which are in substantial conflict with the evolutionary consensus tree of an organism, point to possible horizontal gene transfer events which often delineate significant evolutionary events

Bacterial cooperation through horizontal gene transfer

Cooperation exists across all scales of biological organization, from genetic elements to complex human societies. Bacteria cooperate by secreting molecules that benefit all individuals in the population (i.e., public goods). Genes associated with cooperation can spread among strains through horizontal gene transfer (HGT). We discuss recent findings on how HGT mediated by mobile genetic elements promotes bacterial cooperation, how cooperation in turn can facilitate more frequent HGT, and how the act of HGT itself may be considered as a form of cooperation. We propose that HGT is an important enforcement mechanism in bacterial populations, thus creating a positive feedback loop that further maintains cooperation. To enforce cooperation, HGT serves as a homogenizing force by transferring the cooperative trait, effectively eliminating cheaters

Protocol for an agent-based model of recombination in bacteria playing a public goods game

Agent-based models are composed of individual agents coded for traits, such as cooperation and cheating, that interact in a virtual world based on defined rules. Here, we describe the use of an agent-based model of homologous recombination in bacteria playing a public goods game. We describe steps for software installation, setting model parameters, running and testing models, and visualization and statistical analysis. This protocol is useful in analyses of horizontal gene transfer, bacterial sociobiology, and game theory. For complete details on the use and execution of this protocol, please refer to Lee et al.

The Morphological Content of Ten EDisCS Clusters at 0.5 < z < 0.8

We describe Hubble Space Telescope (HST) imaging of 10 of the 20 ESO Distant Cluster Survey (EDisCS) fields. Each ~40 square arcminute field was imaged in the F814W filter with the Advanced Camera for Surveys Wide Field Camera. Based on these data, we present visual morphological classifications for the ~920 sources per field that are brighter than I_auto=23 mag. We use these classifications to quantify the morphological content of 10 intermediate-redshift (0.5 < z < 0.8) galaxy clusters within the HST survey region. The EDisCS results, combined with previously published data from seven higher redshift clusters, show no statistically significant evidence for evolution in the mean fractions of elliptical, S0, and late-type (Sp+Irr) galaxies in clusters over the redshift range 0.5 < z < 1.2. In contrast, existing studies of lower redshift clusters have revealed a factor of ~2 increase in the typical S0 fraction between z=0.4 and z=0, accompanied by a commensurate decrease in the Sp+Irr fraction and no evolution in the elliptical fraction. The EDisCS clusters demonstrate that cluster morphological fractions plateau beyond z ~ 0.4. They also exhibit a mild correlation between morphological content and cluster velocity dispersion, highlighting the importance of careful sample selection in evaluating evolution. We discuss these findings in the context of a recently proposed scenario in which the fractions of passive (E,S0) and star-forming (Sp,Irr) galaxies are determined primarily by the growth history of clusters.Comment: 18 pages, 7 figures; To be published in ApJ; minor changes made to table label

Stellar SEDs from 0.3-2.5 Microns: Tracing the Stellar Locus and Searching for Color Outliers in SDSS and 2MASS

The Sloan Digital Sky Survey (SDSS) and Two Micron All Sky Survey (2MASS) are rich resources for studying stellar astrophysics and the structure and formation history of the Galaxy. As new surveys and instruments adopt similar filter sets, it is increasingly important to understand the properties of the ugrizJHKs stellar locus, both to inform studies of `normal' main sequence stars as well as for robust searches for point sources with unusual colors. Using a sample of ~600,000 point sources detected by SDSS and 2MASS, we tabulate the position and width of the ugrizJHKs stellar locus as a function of g-i color, and provide accurate polynomial fits. We map the Morgan-Keenan spectral type sequence to the median stellar locus by using synthetic photometry of spectral standards and by analyzing 3000 SDSS stellar spectra with a custom spectral typing pipeline. We develop an algorithm to calculate a point source's minimum separation from the stellar locus in a seven-dimensional color space, and use it to robustly identify objects with unusual colors, as well as spurious SDSS/2MASS matches. Analysis of a final catalog of 2117 color outliers identifies 370 white-dwarf/M dwarf (WDMD) pairs, 93 QSOs, and 90 M giant/carbon star candidates, and demonstrates that WDMD pairs and QSOs can be distinguished on the basis of their J-Ks and r-z colors. We also identify a group of objects with correlated offsets in the u-g vs. g-r and g-r vs. r-i color-color spaces, but subsequent follow-up is required to reveal the nature of these objects. Future applications of this algorithm to a matched SDSS-UKIDSS catalog may well identify additional classes of objects with unusual colors by probing new areas of color-magnitude space.Comment: 23 pages in emulateapj format, 17 figures, 7 tables. Accepted for publication in the Astronomical Journal. To access a high-resolution version of this paper, as well as machine readable tables and an archive of 'The Hammer' spectral typing suite, see http://www.cfa.harvard.edu/~kcovey v2 -- fixed typos in Table 7 (mainly affecting lines for M8-M10 III stars