Which phylogenetic networks are merely trees with additional arcs?

A binary phylogenetic network may or may not be obtainable from a tree by the addition of directed edges (arcs) between tree arcs. Here, we establish a precise and easily tested criterion (based on `2-SAT') that efficiently determines whether or not any given network can be realized in this way. Moreover, the proof provides a polynomial-time algorithm for finding one or more trees (when they exist) on which the network can be based. A number of interesting consequences are presented as corollaries; these lead to some further relevant questions and observations, which we outline in the conclusion.Comment: The final version of this article will appear in Systematic Biology. 20 pages, 7 figure

Genome-scale phylogenetic analysis finds extensive gene transfer among Fungi

Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis we compare the dynamics of genome evolution in two groups of organisms: Cyanobacteria and Fungi. Ancestral genomes are inferred in both clades using two types of methods. First, Count, a gene tree unaware method that models gene duplications, gains and losses to explain the observed numbers of genes present in a genome. Second, ALE, a more recent gene tree-aware method that reconciles gene trees with a species tree using a model of gene duplication, loss, and transfer. We compare their merits and their ability to quantify the role of transfers, and assess the impact of taxonomic sampling on their inferences. We present what we believe is compelling evidence that gene transfer plays a significant role in the evolution of Fungi

The inference of gene trees with species trees

Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can co-exist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice-versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. In this article we review the various models that have been used to describe the relationship between gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree-species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a better basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree-species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution.Comment: Review article in relation to the "Mathematical and Computational Evolutionary Biology" conference, Montpellier, 201

Within-Species Genomic Variation and Variable Patterns of Recombination in the Tetracycline Producer Streptomyces rimosus

Streptomyces rimosus is best known as the primary source of the tetracycline class of antibiotics, most notably oxytetracycline, which have been widely used against many gram-positive and gram-negative pathogens and protozoan parasites. However, despite the medical and agricultural importance of S. rimosus, little is known of its evolutionary history and genome dynamics. In this study, we aim to elucidate the pan-genome characteristics and phylogenetic relationships of 32 S. rimosus genomes. The S. rimosus pan-genome contains more than 22,000 orthologous gene clusters, and approximately 8.8% of these genes constitutes the core genome. A large part of the accessory genome is composed of 9,646 strain-specific genes. S. rimosus exhibits an open pan-genome (decay parameter α = 0.83) and high gene diversity between strains (genomic fluidity φ = 0.12). We also observed strain-level variation in the distribution and abundance of biosynthetic gene clusters (BGCs) and that each individual S. rimosus genome has a unique repertoire of BGCs. Lastly, we observed variation in recombination, with some strains donating or receiving DNA more often than others, strains that tend to frequently recombine with specific partners, genes that often experience recombination more than others, and variable sizes of recombined DNA sequences. We conclude that the high levels of inter-strain genomic variation in S. rimosus is partly explained by differences in recombination among strains. These results have important implications on current efforts for natural drug discovery, the ecological role of strain-level variation in microbial populations, and addressing the fundamental question of why microbes have pan-genomes

The inference of gene trees with species trees.

This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can coexist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree-species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a more reliable basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree-species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution

Bacterial Genome and Population Dynamics with Implications for Public Health

Bacterial populations are extraordinarily heterogeneous. Despite growing clonally, these populations are often composed of multiple lineages distinguished by both phenotypic and genetic differences that are caused by both allelic and whole gene variation. Such genomic mosaicism and within-species variation can significantly impact a species’ response to selective pressures from antibiotic use, vaccination, immune responses and host environment. One important process that contributes to this phenomenon is recombination, the exchange of very similar DNA sequences between strains which can result to either the addition or replacement of homologous genes. Current models of microbial recombination incorporate the null expectation that recombination is a homogeneous process across a species, whereby different lineages of the same species and different genes within a genome exhibit the same rates of DNA donation and receipt. However, recent work has demonstrated that intra-species recombination rates can differ even between strains. This dissertation attempts to elucidate the extent of, and the processes underlying, heterogeneity in genomic content in microbial species and populations relevant to human health. The first chapter addresses the best-known producer of the tetracycline class of antibiotics, Streptomyces rimosus. Results suggest that even strains appearing nearly identical in a core-genome phylogeny have divergent biosynthetic gene cluster content, emphasizing the importance of analyzing entire populations in drug discovery protocols. The second chapter explores the population dynamics of one of the most common causes of foodborne illness in the world, Salmonella enterica with results that indicate the evolution of ecologically unique subspecies of S. enterica are intricately linked by heterogeneous recombination. The third and fourth chapters demonstrate similar patterns of genomic diversity and recombination of clinically relevant genes in populations of Campylobacter jejuni and S. enterica collected from hospitals in New Hampshire in 2017. Finally, the fifth chapter describes a novel bioinformatic program called HERO which rapidly identifies and visualizes donor-recipient recombination pairs from a bacterial population. It also reports measures of heterogeneity in the population’s total recombination including events per donor-recipient pair, recombined DNA fragment length and the number of events per gene. Collectively, these results contribute to the growing evidence that intra-species heterogeneity plays a role in the evolution and management of bacterial species associated with public health

Bacterial Genome and Population Dynamics with Implications for Public Health

Bacterial populations are extraordinarily heterogeneous. Despite growing clonally, these populations are often composed of multiple lineages distinguished by both phenotypic and genetic differences that are caused by both allelic and whole gene variation. Such genomic mosaicism and within-species variation can significantly impact a species’ response to selective pressures from antibiotic use, vaccination, immune responses and host environment. One important process that contributes to this phenomenon is recombination, the exchange of very similar DNA sequences between strains which can result to either the addition or replacement of homologous genes. Current models of microbial recombination incorporate the null expectation that recombination is a homogeneous process across a species, whereby different lineages of the same species and different genes within a genome exhibit the same rates of DNA donation and receipt. However, recent work has demonstrated that intra-species recombination rates can differ even between strains. This dissertation attempts to elucidate the extent of, and the processes underlying, heterogeneity in genomic content in microbial species and populations relevant to human health. The first chapter addresses the best-known producer of the tetracycline class of antibiotics, Streptomyces rimosus. Results suggest that even strains appearing nearly identical in a core-genome phylogeny have divergent biosynthetic gene cluster content, emphasizing the importance of analyzing entire populations in drug discovery protocols. The second chapter explores the population dynamics of one of the most common causes of foodborne illness in the world, Salmonella enterica with results that indicate the evolution of ecologically unique subspecies of S. enterica are intricately linked by heterogeneous recombination. The third and fourth chapters demonstrate similar patterns of genomic diversity and recombination of clinically relevant genes in populations of Campylobacter jejuni and S. enterica collected from hospitals in New Hampshire in 2017. Finally, the fifth chapter describes a novel bioinformatic program called HERO which rapidly identifies and visualizes donor-recipient recombination pairs from a bacterial population. It also reports measures of heterogeneity in the population’s total recombination including events per donor-recipient pair, recombined DNA fragment length and the number of events per gene. Collectively, these results contribute to the growing evidence that intra-species heterogeneity plays a role in the evolution and management of bacterial species associated with public health

Vida microbiana a temperaturas elevadas. Diversidad, aislamiento, termoestabilidad molecular y genómica

A pesar de los numerosos estudios publicados sobre la vida a altas temperaturas, aún existen aspectos fundamentales por comprender. La presente tesis estudia la vida microbiana a altas temperaturas desde diferentes enfoques. Por un lado, analizamos la influencia de la temperatura sobre la distribución de los microorganismos tomando como modelo un gradiente de temperatura natural de 50ºC en una fuente termal. La temperatura y las interacciones entre sus componentes resultaron ser determinantes para estructurar las comunidades microbianas. El aislamiento de una nueva especie de bacteria termófila extrema y anaeróbica, Fervidobacterium thailandense FC2004T, y la secuenciación de su genoma hace posible un estudio en detalle y su clasificación taxonómica. La comparación de cuatro genomas dentro del género Fervidobacterium ha permitido determinar que los genes que codifican transposasas son un modelo adecuado para analizar fenómenos de intercambio de material genético. (transferencia horizontal de genes, HGT) y evaluar la plasticidad de estos genomas y su historia evolutiva. Los microorganismos termófilos viven a temperaturas a las que numerosas biomoléculas, como el NADH, son inestables. La viscosidad influye decisivamente en la estabilización de esas pequeñas biomoléculas. La viscosidad intracelular en microorganismos termófilos (entre 50 y 80ºC) era relativamente elevada, lo que confirma el efecto estabilizador de la viscosidad. Esta tesis contribuye a comprender la importancia de la temperatura sobre los microorganismos y sus comunidades microbianas, su capacidad para desarrollarse a temperaturas elevadas, así como el dinamismo de sus genomas y fenotipos