Inversion-based genomic signatures

<p>Abstract</p> <p>Background</p> <p>Reconstructing complete ancestral genomes (at least in terms of their gene inventory and arrangement) is attracting much interest due to the rapidly increasing availability of whole genome sequences. While modest successes have been reported for mammalian and even vertebrate genomes, more divergent groups continue to pose a stiff challenge, mostly because current models of genomic evolution support too many choices.</p> <p>Results</p> <p>We describe a novel type of genomic signature based on rearrangements that characterizes evolutionary changes that must be common to all minimal rearrangement scenarios; by focusing on global patterns of rearrangements, such signatures bypass individual variations and sharply restrict the search space. We present the results of extensive simulation studies demonstrating that these signatures can be used to reconstruct accurate ancestral genomes and phylogenies even for widely divergent collections.</p> <p>Conclusion</p> <p>Focusing on genome triples rather than genomes pairs unleashes the full power of evolutionary analysis. Our genomic signature captures shared evolutionary events and thus can form the basis of a robust analysis and reconstruction of evolutionary history.</p

A framework for orthology assignment from gene rearrangement data

Abstract. Gene rearrangements have successfully been used in phylogenetic reconstruction and comparative genomics, but usually under the assumption that all genomes have the same gene content and that no gene is duplicated. While these assumptions allow one to work with organellar genomes, they are too restrictive when comparing nuclear genomes. The main challenge is how to deal with gene families, specifically, how to identify orthologs. While searching for orthologies is a common task in computational biology, it is usually done using sequence data. We approach that problem using gene rearrangement data, provide an optimization framework in which to phrase the problem, and present some preliminary theoretical results.

A Methodological Framework for the Reconstruction of Contiguous Regions of Ancestral Genomes and Its Application to Mammalian Genomes

The reconstruction of ancestral genome architectures and gene orders from homologies between extant species is a long-standing problem, considered by both cytogeneticists and bioinformaticians. A comparison of the two approaches was recently investigated and discussed in a series of papers, sometimes with diverging points of view regarding the performance of these two approaches. We describe a general methodological framework for reconstructing ancestral genome segments from conserved syntenies in extant genomes. We show that this problem, from a computational point of view, is naturally related to physical mapping of chromosomes and benefits from using combinatorial tools developed in this scope. We develop this framework into a new reconstruction method considering conserved gene clusters with similar gene content, mimicking principles used in most cytogenetic studies, although on a different kind of data. We implement and apply it to datasets of mammalian genomes. We perform intensive theoretical and experimental comparisons with other bioinformatics methods for ancestral genome segments reconstruction. We show that the method that we propose is stable and reliable: it gives convergent results using several kinds of data at different levels of resolution, and all predicted ancestral regions are well supported. The results come eventually very close to cytogenetics studies. It suggests that the comparison of methods for ancestral genome reconstruction should include the algorithmic aspects of the methods as well as the disciplinary differences in data aquisition

Evolution of whole genomes through inversions:models and algorithms for duplicates, ancestors, and edit scenarios

Advances in sequencing technology are yielding DNA sequence data at an alarming rate – a rate reminiscent of Moore's law. Biologists' abilities to analyze this data, however, have not kept pace. On the other hand, the discrete and mechanical nature of the cell life-cycle has been tantalizing to computer scientists. Thus in the 1980s, pioneers of the field now called Computational Biology began to uncover a wealth of computer science problems, some confronting modern Biologists and some hidden in the annals of the biological literature. In particular, many interesting twists were introduced to classical string matching, sorting, and graph problems. One such problem, first posed in 1941 but rediscovered in the early 1980s, is that of sorting by inversions (also called reversals): given two permutations, find the minimum number of inversions required to transform one into the other, where an inversion inverts the order of a subpermutation. Indeed, many genomes have evolved mostly or only through inversions. Thus it becomes possible to trace evolutionary histories by inferring sequences of such inversions that led to today's genomes from a distant common ancestor. But unlike the classic edit distance problem where string editing was relatively simple, editing permutation in this way has proved to be more complex. In this dissertation, we extend the theory so as to make these edit distances more broadly applicable and faster to compute, and work towards more powerful tools that can accurately infer evolutionary histories. In particular, we present work that for the first time considers genomic distances between any pair of genomes, with no limitation on the number of occurrences of a gene. Next we show that there are conditions under which an ancestral genome (or one close to the true ancestor) can be reliably reconstructed. Finally we present new methodology that computes a minimum-length sequence of inversions to transform one permutation into another in, on average, O(n log n) steps, whereas the best worst-case algorithm to compute such a sequence uses O(n√n log n) steps

Evolutionary Dynamics Of Mitochondrial Mutations In The Origin And Development Of Eukaryotic Sex

Sexual reproduction is virtually universal among eukaryotes, suggesting that the last eukaryotic common ancestor was already sexual. It is very likely that the first sexual lineage already contained mitochondrial endosymbionts, each with its own genome of bacterial origin. In this thesis I develop a set of theoretical models that together form a framework for understanding the evolution of eukaryotic sex and further sexual traits— mating types, uniparental inheritance, sexual dimorphism and the early sequestration of a protected germline in higher metazoans—as a consequence of mitochondrial endosymbiosis. First, I review currently dominating views on the origin of eukaryotes and selective forces that led to the evolution of meiotic sex early in the prokaryote- eukaryote transition. Sex likely emerged as a direct consequence of the mitochondrial endosymbiosis, and was essential for the further evolution of eukaryotic genome complexity. In Chapter 2, I show that the evolution of sexual cell fusion in the nascent eukaryotic lineage might have been driven by cytoplasmic mixing, temporarily masking the detrimental effects of defective organelles. The model introduced in Chapter 3 shows that self-incompatible mating types can evolve to ensure the efficient removal of mitochondrial mutations through asymmetric organelle transmission. Frequent observations of paternal leakage and heteroplasmy pose a substantial challenge to the current understanding of uniparental organelle inheritance. In Chapter 4 I show that the evolutionarily stable pattern of cytoplasmic inheritance depends on which sex—male or female—governs the destruction of paternal organelles. Maternal regulation favours complete elimination of sperm mitochondria, while paternal control supports paternal leakage and heteroplasmy. Intersexual competition over the control of cytoplasmic inheritance may have driven the repeated evolution of mechanisms enforcing uniparental inheritance. Finally, I analyse the dynamics of mitochondrial mutation segregation in the evolution of the metazoan germline. High mitochondrial DNA replication error rates in bilaterians favour early germline sequestration, while in basal metazoans gamete quality is maximized through repeated cell divisions in non-sequestered germline stem cell lineages

Phototrophic Bacteria

Microorganisms is pleased to publish this book, which reprints papers that appeared in a Special Issue on “Phototrophic Bacteria”, with Guest Editors Robert Blankenship and Matthew Sattley. This Special Issue included research on all types of phototrophic bacteria, including both anoxygenic and oxygenic forms. Research on these bacterial organisms has greatly advanced our understanding of the basic principles that underlie the energy storage that takes place in all types of photosynthetic organisms, including both bacterial and eukaryotic forms. Topics of interest include: microbial physiology, microbial ecology, microbial genetics, evolutionary microbiology, systems microbiology, agricultural microbiology, microbial biotechnology, and environmental microbiology, as all are related to phototrophic bacteria

Phylogeography of Austral soil invertebrates

Soil invertebrates are terrestrial animals belonging to ancient phyla that emerged almost half a billion years ago. They have since spread throughout all known landmasses, with contemporary distributions governed by geological and environmental change across spatial and temporal gradients across the globe. However, limited knowledge of southern hemisphere (Austral) species hampers our ability to discern the general patterns of distribution and speciation. The lack of robust taxonomic information has also constrained our understanding of the evolutionary relationships and functional roles of the diverse soil fauna. This thesis capitalises on the development in molecular tools and improved sequence libraries to explore the factors that define the distribution and diversity of common soil invertebrates, specifically oribatid mites (Acari), springtails (Collembola) and nematodes (Nematoda). I investigated communities at continental-scales from maritime Antarctica and Australia to enable greater resolution of the drivers of distribution that might be applicable to southern hemisphere taxa more broadly. In a literature review I introduce the bioinformatic approaches using phylogeography to resolve evolutionary theories concerning soil fauna indigenous to Antarctica. Phylogenetic evidence supports most soil faunal groups as having ancient origins, refugial survival and repeated colonisation, whilst also highlighting the benefits of comparative analyses over larger scales. In addition, I show in a perspectives paper that morphological and functional traits are phylogenetically constrained in nematodes and springtails, allowing function to be partially conferred for ‘unknown’ species using sequencing approaches. Baseline biodiversity across a transect through maritime Antarctica found contrasting distributions of mites and springtails and the influences of climatic factors at broad scales and soil microhabitat conditions at local scales. Detailed population genetic analysis of genotypes of the oribatid mites Podacarus auberti and Membranoppia loxolineata alongside the springtail Cryptopygus antarcticus revealed the importance of multiple dispersal events in their ancestral past, supporting theories of refugial survival. Comparative analysis of phylogeographic reconstructions with an analogous Australian transect highlighted that the importance of dispersal differs among mites and springtails and supported the influences of climate and edaphic factors on assemblage structure. These different influences of biogeography and climatic variability related to inherent morphological and physiological traits of the study organisms demonstrate potentially contrasting responses to future episodes of environmental change. With such knowledge, conservation strategies of Austral soil fauna can be re-focussed to ensure their continued persistence in terrestrial ecosystems