Mitochondria are organelles present in most eukaryotic cells. They generate most of the cells adenosine triphosphate (ATP) supply which make them essential for cell viability. It is assumed that they are derived from a proteobacterial ancestor as they retain their own, drastically small genome. The importance in studying mitochondrial genome evolution came from the discovery of a large number of human diseases that are caused by mitochondrial dysfunction (e.g., Parkinson and Alzheimer). Many of these diseases are a result of a mutation in one of the mitochondrial genes or a defective mitochondrial DNA (mtDNA) maintenance, mostly caused by genetic defects in proteins involved in mtDNA replication. In order to explore the diversity and understand the evolution of mitochondrial genomes (mitogenomes) in animals, multiple methods have been developed in this study to deal with two biological problems related to the mitochondrial genome evolution. A new method for identifying the mitochondrial origins of replication is presented. This method deals with the problem of determining the origins of replication, which despite many previous efforts has remained non-trivial even in the small genomes of animal mitochondria. The replication mechanism is of central interest to understand the evolution of mitochondrial genomes since it allows the duplication of the genetic information. The extensive work that has been done to study the replication of mitochondrial genomes has generated the assumption of the strand displacement model (SDM) also known as the standard model of replication that is known to leave the mitochondrial H-strand in a single stranded state exposing it to mutation and damage. Later on, other models of replication have been suggested such as the strand coupled bidirectional replication model, its refinement which assumes the bidirectional mode but with a unidirectional start, and the \"RNA incorporation throughout the lagging strand\" (RITOLS) model proposed as a refinement of the strand displacement model. Based on the observation that the GC-skew is correlated with the distance from the replication origins in the light of the strand displacement model of replication, a new computational method to infer the position of both the heavy strand and the light strand origins from nucleotide skew data has been developed. The method has been applied in a comprehensive survey of deuterostome mitochondria where conserved positions of the replication origins for the vast majority of vertebrates and cephalochordates have been inferred. Deviations from the consensus picture are presumably associated with genome rearrangements. Additionally, two methods for the identification of tRNA remolding events throughout Metazoa have been developed. Remolding changes the identity of a tRNA by a duplication and a point mutation(s) of the anticodon. This new tRNA takes the identity of another tRNA which is then lost. This can lead to artifacts in the annotation of mitogenomes and thus in studies of mitogenomic evolution. In this work, novel methods are developed to detect tRNA remolding in large-scale data sets. The first method represents an extension of the similarity-based approach to determine remolding candidates with high confidence. This approach uses an extended set of criteria based on both sequence and structural similarities of the tRNAs in conjunction with statistical tests. The second method is a novel phylogeny-based likelihood method which evaluates specific topologies of gene phylogenies of the two tRNA families relevant to a putative remolding event. Both methods have been applied to survey tRNA remolding throughout animal evolution. At least three novel remolding events are identified in addition to the ones previously mentioned in the literature. A detailed analysis of these remoldings showed that many of them are derived ancestral events.

Background: Transfer RNAs (tRNAs) are ubiquitous in all living organism. They implement the genetic code so that most genomes contain distinct tRNAs for almost all 61 codons. They behave similar to mobile elements and proliferate in genomes spawning both local and non-local copies. Most tRNA families are therefore typically present as multicopy genes. The members of the individual tRNA families evolve under concerted or rapid birth-death evolution, so that paralogous copies maintain almost identical sequences over long evolutionary time-scales. To a good approximation these are functionally equivalent. Individual tRNA copies thus are evolutionary unstable and easily turn into pseudogenes and disappear. This leads to a rapid turnover of tRNAs and often large differences in the tRNA complements of closely related species. Since tRNA paralogs are not distinguished by sequence, common methods cannot not be used to establish orthology between tRNA genes. Results: In this contribution we introduce a general framework to distinguish orthologs and paralogs in gene families that are subject to concerted evolution. It is based on the use of uniquely aligned adjacent sequence elements as anchors to establish syntenic conservation of sequence intervals. In practice, anchors and intervals can be extracted from genome-wide multiple sequence alignments. Syntenic clusters of concertedly evolving genes of different families can then be subdivided by list alignments, leading to usually small clusters of candidate co-orthologs. On the basis of recent advances in phylogenetic combinatorics, these candidate clusters can be further processed by cograph editing to recover their duplication histories. We developed a workflow that can be conceptualized as stepwise refinement of a graph of homologous genes. We apply this analysis strategy with different types of synteny anchors to investigate the evolution of tRNAs in primates and fruit flies. We identified a large number of tRNA remolding events concentrated at the tips of the phylogeny. With one notable exception all phylogenetically old tRNA remoldings do not change the isoacceptor class. Conclusions: Gene families evolving under concerted evolution are not amenable to classical phylogenetic analyses since paralogs maintain identical, species-specific sequences, precluding the estimation of correct gene trees from sequence differences. This leaves conservation of syntenic arrangements with respect to "anchor elements" that are not subject to concerted evolution as the only viable source of phylogenetic information. We have demonstrated here that a purely synteny-based analysis of tRNA gene histories is indeed feasible. Although the choice of synteny anchors influences the resolution in particular when tight gene clusters are present, and the quality of sequence alignments, genome assemblies, and genome rearrangements limits the scope of the analysis, largely coherent results can be obtained for tRNAs. In particular, we conclude that a large fraction of the tRNAs are recent copies. This proliferation is compensated by rapid pseudogenization as exemplified by many very recent alloacceptor remoldings.

Mitochondria are organelles present in most eukaryotic cells. They generate most of the cells adenosine triphosphate (ATP) supply which make them essential for cell viability. It is assumed that they are derived from a proteobacterial ancestor as they retain their own, drastically small genome. The importance in studying mitochondrial genome evolution came from the discovery of a large number of human diseases that are caused by mitochondrial dysfunction (e.g., Parkinson and Alzheimer). Many of these diseases are a result of a mutation in one of the mitochondrial genes or a defective mitochondrial DNA (mtDNA) maintenance, mostly caused by genetic defects in proteins involved in mtDNA replication. In order to explore the diversity and understand the evolution of mitochondrial genomes (mitogenomes) in animals, multiple methods have been developed in this study to deal with two biological problems related to the mitochondrial genome evolution. A new method for identifying the mitochondrial origins of replication is presented. This method deals with the problem of determining the origins of replication, which despite many previous efforts has remained non-trivial even in the small genomes of animal mitochondria. The replication mechanism is of central interest to understand the evolution of mitochondrial genomes since it allows the duplication of the genetic information. The extensive work that has been done to study the replication of mitochondrial genomes has generated the assumption of the strand displacement model (SDM) also known as the standard model of replication that is known to leave the mitochondrial H-strand in a single stranded state exposing it to mutation and damage. Later on, other models of replication have been suggested such as the strand coupled bidirectional replication model, its refinement which assumes the bidirectional mode but with a unidirectional start, and the \"RNA incorporation throughout the lagging strand\" (RITOLS) model proposed as a refinement of the strand displacement model. Based on the observation that the GC-skew is correlated with the distance from the replication origins in the light of the strand displacement model of replication, a new computational method to infer the position of both the heavy strand and the light strand origins from nucleotide skew data has been developed. The method has been applied in a comprehensive survey of deuterostome mitochondria where conserved positions of the replication origins for the vast majority of vertebrates and cephalochordates have been inferred. Deviations from the consensus picture are presumably associated with genome rearrangements. Additionally, two methods for the identification of tRNA remolding events throughout Metazoa have been developed. Remolding changes the identity of a tRNA by a duplication and a point mutation(s) of the anticodon. This new tRNA takes the identity of another tRNA which is then lost. This can lead to artifacts in the annotation of mitogenomes and thus in studies of mitogenomic evolution. In this work, novel methods are developed to detect tRNA remolding in large-scale data sets. The first method represents an extension of the similarity-based approach to determine remolding candidates with high confidence. This approach uses an extended set of criteria based on both sequence and structural similarities of the tRNAs in conjunction with statistical tests. The second method is a novel phylogeny-based likelihood method which evaluates specific topologies of gene phylogenies of the two tRNA families relevant to a putative remolding event. Both methods have been applied to survey tRNA remolding throughout animal evolution. At least three novel remolding events are identified in addition to the ones previously mentioned in the literature. A detailed analysis of these remoldings showed that many of them are derived ancestral events.

Uniaxial consolidation experiments on Mass Transport Deposit (MTD) and non-MTD core samples from Ursa Basin, Gulf of Mexico, show MTDs have a lower porosity at a given effective stress compared to adjacent non-MTD sediments; a behavior observed in additional experiments on lab remolded Ursa core and resedimented Boston Blue Clay (BBC). I hypothesize debris flow action remolded the sediment: removing its stress history through shearing action, resulting in dense sediments at shallow depth. I supplement testing this hypothesis through lab remolding of BBC (in addition to Ursa clay) due to the greater availability and knowledge of this material. Ursa MTDs record multiple submarine slope failure events within the upper 200 meters below sea floor (mbsf); the most prominent is labeled MTD-2. MTDs have lower porosity and higher bulk density than surrounding, non-MTD, sediment. Porosity ([phi]) is 52% at 125mbsf – immediately below MTD-2; whereas [phi] is 46% at 115mbsf – within MTD-2. Comparison of non-MTD samples to MTD-2 samples, and intact to remolded samples, shows a decrease in sediment compressibility (Cc) within the MTD-2 and remolded sediments. Permeability within Ursa mudstones also declines with porosity according to: log (k) = A[phi] - B. Permeability is slightly higher within MTD-2; however grain size analysis indicates lower clay content in MTD-2 versus the non-MTDs. Pre-consolidation stress interpretations from the experiments show a linear trend in both MTD and non-MTD sediments, indicating both geologic units depict the same pore pressure profile. Remolding via debris flow explains the origin of MTDs at Ursa and governs the evolution of this geologic unit to its dense, highly consolidated, state today. At some point, slope failure triggered movement of the sediment down slope in form of a debris flow. The shearing action of the debris flow weakened the sediment, reducing its ability to support the overburden. As consolidation resumed, the remolded sediment followed a new, less steep, Cc curve. Within the geologic record, a distinctive dense, shallow unit is preserved; evidence for historical slope failure. / text

Background: Transfer RNAs (tRNAs) are ubiquitous in all living organism. They implement the genetic code so that most genomes contain distinct tRNAs for almost all 61 codons. They behave similar to mobile elements and proliferate in genomes spawning both local and non-local copies. Most tRNA families are therefore typically present as multicopy genes. The members of the individual tRNA families evolve under concerted or rapid birth-death evolution, so that paralogous copies maintain almost identical sequences over long evolutionary time-scales. To a good approximation these are functionally equivalent. Individual tRNA copies thus are evolutionary unstable and easily turn into pseudogenes and disappear. This leads to a rapid turnover of tRNAs and often large differences in the tRNA complements of closely related species. Since tRNA paralogs are not distinguished by sequence, common methods cannot not be used to establish orthology between tRNA genes. Results: In this contribution we introduce a general framework to distinguish orthologs and paralogs in gene families that are subject to concerted evolution. It is based on the use of uniquely aligned adjacent sequence elements as anchors to establish syntenic conservation of sequence intervals. In practice, anchors and intervals can be extracted from genome-wide multiple sequence alignments. Syntenic clusters of concertedly evolving genes of different families can then be subdivided by list alignments, leading to usually small clusters of candidate co-orthologs. On the basis of recent advances in phylogenetic combinatorics, these candidate clusters can be further processed by cograph editing to recover their duplication histories. We developed a workflow that can be conceptualized as stepwise refinement of a graph of homologous genes. We apply this analysis strategy with different types of synteny anchors to investigate the evolution of tRNAs in primates and fruit flies. We identified a large number of tRNA remolding events concentrated at the tips of the phylogeny. With one notable exception all phylogenetically old tRNA remoldings do not change the isoacceptor class. Conclusions: Gene families evolving under concerted evolution are not amenable to classical phylogenetic analyses since paralogs maintain identical, species-specific sequences, precluding the estimation of correct gene trees from sequence differences. This leaves conservation of syntenic arrangements with respect to "anchor elements" that are not subject to concerted evolution as the only viable source of phylogenetic information. We have demonstrated here that a purely synteny-based analysis of tRNA gene histories is indeed feasible. Although the choice of synteny anchors influences the resolution in particular when tight gene clusters are present, and the quality of sequence alignments, genome assemblies, and genome rearrangements limits the scope of the analysis, largely coherent results can be obtained for tRNAs. In particular, we conclude that a large fraction of the tRNAs are recent copies. This proliferation is compensated by rapid pseudogenization as exemplified by many very recent alloacceptor remoldings.