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How does the interplay between selection, mutation and horizontal gene transfer modify the phenotypic distribution of a bacterial or cell population? While horizontal gene transfer, which corresponds to the exchange of genetic material between individuals, has a major role in the adaptation of many organisms, its impact on the phenotypic density of populations is not yet fully understood.

We study an elliptic integro-differential equation describing the evolutionary equilibrium of the phenotypic density of an asexual population. In a regime of small mutational variance, we characterize the solution which results from the balance between competition for a resource, mutation and horizontal gene transfer. We show that in a certain range of parameters polymorphic equilibria exist, which means that the phenotypic density may concentrate around several dominant traits. Such polymorphic equilibria result from an antagonist interplay between horizontal gene transfer and selection, while similar models which neglect the transfer lead only to monomorphic equilibria.

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.

Horizontal gene transfer (HGT) is the event of transferring genetic material from one lineage in the evolutionary tree to a different lineage. HGT plays a major role in bacterial genome diversification and is a significant mechanism by which bacteria develop resistance to antibiotics. Although the prevailing assumption is of complete HGT, cases of partial HGT (which are also named chimeric HGT) where only part of a gene is horizontally transferred, have also been reported, albeit less frequently. In this work we suggest a new probabilistic model, the NET-HMM, for analyzing and modeling phylogenetic networks. This new model captures the biologically realistic assumption that neighboring sites of DNA or amino acid sequences are not independent, which increases the accuracy of the inference. The model describes the phylogenetic network as a Hidden Markov Model (HMM), where each hidden state is related to one of the network's trees. One of the advantages of the NET-HMM is its ability to infer partial HGT as well as complete HGT. We describe the properties of the NET-HMM, devise efficient algorithms for solving a set of problems related to it, and implement them in software. We also provide a novel complementary significance test for evaluating the fitness of a model (NET-HMM) to a given dataset. Using NET-HMM, we are able to answer interesting biological questions, such as inferring the length of partial HGT's and the affected nucleotides in the genomic sequences, as well as inferring the exact location of HGT events along the tree branches. These advantages are demonstrated through the analysis of synthetical inputs and three different biological inputs.

We propose an original program "Evolutionary constructor" that is capable of computationally efficient modeling of both population-genetic and ecological problems, combining these directions in one model of required detail level. We also present results of comparative modeling of stability, adaptability and biodiversity dynamics in populations of unicellular haploid organisms which form symbiotic ecosystems. The advantages and disadvantages of two evolutionary strategies of biota formation — a few generalists' taxa-based biota formation and biodiversity-based biota formation — are discussed.

Seventy-eight promoter islands with an extraordinarily high density of potential promoters have been recently found in the genome of Escherichia coli. It has been shown that RNA polymerase binds internal promoters of these islands and produces short oligonucleotides, while the synthesis of normal mRNAs is suppressed. This quenching may be biologically relevant, as most islands are associated with foreign genes, which expression may deplete cellular resources. However, a molecular mechanism of silencing with the participation of these promoter-rich regions remains obscure. It has been demonstrated that all islands interact with histone-like protein H-NS — a specific sentinel of foreign genes. In this study, we demonstrated the inhibitory effect of H-NS using Δhns mutant of Escherichia coli and showed that deletion of dps, encoding another protein of bacterial nucleoid, tended to decrease rather than increase the amount of island-specific transcripts. This observation precluded consideration of promoter islands as sites for targeted heterochromatization only and a computer search for the binding sites of 53 transcription factors (TFs) revealed six proteins, which may specifically regulate their transcriptional output.

Palindromes are frequently underrepresented in prokaryotic genomes. Palindromic 5${}^{\prime }$-GATC-3${}^{\prime }$ site is a recognition site of different Restriction-Modification (R-M) systems, as well as solitary methyltransferase Dam. Classical GATC-specific R-M systems methylate GATC and cleave unmethylated GATC. On the contrary, methyl-directed Type II restriction endonucleases cleave methylated GATC. Methylation of GATC by Dam methyltransferase is involved in the regulation of different cellular processes. The diversity of functions of GATC-recognizing proteins makes GATC sequence a good model for studying the reasons of palindrome avoidance in prokaryotic genomes.

In this work, the influence of R-M systems and solitary proteins on the GATC site avoidance is described by a mathematical model. GATC avoidance is strongly associated with the presence of alternate (methyl-directed or classical Type II R-M system) genes in different strains of the same species, as we have shown for Streptococcus pneumoniae, Neisseria meningitidis, Eubacterium rectale, and Moraxella catarrhalis. We hypothesize that GATC avoidance can result from a DNA exchange between strains with different methylation status of GATC site within the process of natural transformation. If this hypothesis is correct, the GATC avoidance is a sign of a DNA exchange between bacteria with different methylation status in a mixed population.

This paper presents a mathematical model for bacterial growth, mutations, horizontal transfer and development of antibiotic resistance. The model is based on the so-called kinetic theory for active particles that is able to capture the main complexity features of the system. Bacterial and immune cells are viewed as active particles whose microscopic state is described by a scalar variable. Particles interact among them and the temporal evolution of the system is described by a generalized distribution function over the microscopic state. The model is derived and tested in a couple of case studies in order to confirm its ability to describe one of the most fundamental problems of modern medicine, namely bacterial resistance to antibiotics.

The SPR (subtree prune and regraft) operation is used as the basis for reconciling incongruent phylogenetic trees, particularly for detecting and analyzing non-treelike evolutionary histories such as horizontal gene transfer, hybrid speciation, and recombination. The SPR-based tree reconciliation problem has been shown to be NP-hard, and several efficient heuristics have been designed to solve it. A major drawback of these heuristics is that for the most part they do not handle non-binary trees appropriately. Further, their computational efficiency suffers significantly when computing multiple optimal reconciliations. In this paper, we present algorithmic techniques for efficient SPR-based reconciliation of trees that are not necessarily binary. Further, we present divide-and-conquer approaches that enable efficient computing of multiple optimal reconciliations. We have implemented our techniques in the PhyloNet software package, which is publicly available at http://bioinfo.cs.rice.edu. The resulting method outperforms all existing methods in terms of speed, and performs at least as well as those methods in terms of accuracy.

Non-point source microbial pollution damages the overall health of marine ecosystems. Beyond their direct effects, contaminating microbes can introduce antimicrobial resistance and virulence genes into resident species by horizontal gene transfer, a process that may be enhanced by co-pollutants such as heavy metals. In this work, a number of heavy metal- and antimicrobial-resistant (AMR) strains of E. coli were isolated from water and sediment samples collected in the Causeway Bay, Hong Kong (22.2833 N, 114.1847 E) and their complete genomes obtained by hybrid assembly using both Illumina MiSeq and Oxford Nanopore MinION sequencing platforms. Genomic analysis showed an abundance of plasmids and mobile elements bearing heavy metal- and AMR genes, such as the mer operon and tetR-tetA efflux system, with these features frequently co-located. In addition, NCBIBLAST–using isolates collected from in-land soil, freshwater, and animal faeces in Hong Kong, as well as the NCBI database – showed that these genes, while common amongst human and animal-derived Enterobacteriaceae, could also be shown present in a number of strains of obligate halophilic Vibrio spp.. Previous water chemistry analysis at this location showed high levels of heavy metal contamination (98 ppm Pb, 0.12 ppm Hg, and 0.4 ppm Cd), which has been shown to promote AMR transfer by selecting for co- resistance. Further isolation and characterisation of marine bacterial species from Hong Kong coastal waters will help to determine the extent of this process.

Knowledge on the evolution of symbiotic bacteria elicited by their co-migration with host plants into the novel soil/climatic environments should be used as a conduit for constructing the beneficial plant-microbial systems applied in sustainable agriculture. Co-migration of leguminous plants and nodule bacteria (rhizobia) from the centers of origins into cropping areas often results in generating the Novel Symbionts (NS) via the “symbiotic” gene transfer from initial symbionts to the local soil or plant-associated bacteria. NS usually combine the low/zero activity of N₂ fixation with the high competitiveness for soil and nodular niches blocking the inoculation of leguminous crops by commercial strains. Mathematical simulation of legume-rhizobia interactions suggests that this effect may be due to retarding the evolution of NS towards the elevated N₂-fixing activity. Construction of co-adapted “gene-for-gene” systems is a promising approach to ensure the competitive advantage of effective (commercial) rhizobia strains over the ineffective (NS, local) strains. This advantage may be ensured also by engineering the genes responsible for soil adaptations and nodulation competitiveness into the rhizobia genotypes capable of active N₂ fixation.

The theory of cometary panspermia, developed by the late Sir Fred Hoyle and the present author argues that life originated cosmically as a unique event in one of a great multitude of comets or planetary bodies in the Universe. Life on Earth did not originate here but was introduced by impacting comets, and its further evolution was driven by the subsequent acquisition of cosmically derived genes. Explicit predictions of this theory published in 1979–1981, stating how the acquisition of new genes drives evolution, are compared with recent developments in relation to horizontal gene transfer, and the role of retroviruses in evolution. Precisely-stated predictions of the theory of cometary panspermia are shown to have been verified.