The rhizome of Reclinomonas americana, Homo sapiens, Pediculus humanus and Saccharomyces cerevisiae mitochondria

<p>Abstract</p> <p>Background</p> <p>Mitochondria are thought to have evolved from eubacteria-like endosymbionts; however, the origin of the mitochondrion remains a subject of debate. In this study, we investigated the phenomenon of chimerism in mitochondria to shed light on the origin of these organelles by determining which species played a role in their formation. We used the mitochondria of four distinct organisms, <it>Reclinomonas americana</it>, <it>Homo sapiens</it>, <it>Saccharomyces cerevisiae </it>and multichromosome <it>Pediculus humanus</it>, and attempted to identify the origin of each mitochondrial gene.</p> <p>Results</p> <p>Our results suggest that the origin of mitochondrial genes is not limited to the <it>Rickettsiales </it>and that the creation of these genes did not occur in a single event, but through multiple successive events. Some of these events are very old and were followed by events that are more recent and occurred through the addition of elements originating from current species. The points in time that the elements were added and the parental species of each gene in the mitochondrial genome are different to the individual species. These data constitute strong evidence that mitochondria do not have a single common ancestor but likely have numerous ancestors, including proto-<it>Rickettsiales</it>, proto-<it>Rhizobiales </it>and proto-<it>Alphaproteobacteria</it>, as well as current alphaproteobacterial species. The analysis of the multichromosome <it>P. humanus </it>mitochondrion supports this mechanism.</p> <p>Conclusions</p> <p>The most plausible scenario of the origin of the mitochondrion is that ancestors of <it>Rickettsiales </it>and <it>Rhizobiales </it>merged in a proto-eukaryotic cell approximately one billion years ago. The fusion of the <it>Rickettsiales </it>and <it>Rhizobiales </it>cells was followed by gene loss, genomic rearrangements and the addition of alphaproteobacterial elements through ancient and more recent recombination events. Each gene of each of the four studied mitochondria has a different origin, while in some cases, multichromosomes may allow for enhanced gene exchange. Therefore, the tree of life is not sufficient to explain the chimeric structure of current genomes, and the theory of a single common ancestor and a top-down tree does not reflect our current state of knowledge. Mitochondrial evolution constitutes a rhizome, and it should be represented as such.</p> <p>Reviewers</p> <p>This article was revised by William Martin, Arcady Mushegian and Eugene V. Koonin.</p

Spatial effects in multivariate ARCH

This paper proposes a new approach for the specification of multivariate GARCH models for data sets with a potentially large cross-section dimension. The approach exploits the spatial dependence structure associated with asset characteristics, like industrial sectors and capitalization size. We use the acronym SEARCH for this model, short for Spatial Effects in ARCH. This parametrization extends current feasible specifications for large scale GARCH models, while keeping the numbers of parameters linear with respect to the number of assets. An application to daily returns on 20 stocks from the NYSE for the period January 1994 to June 2001 shows the benefits of the present specification.

Testing the use of molluscs to infer climate with special reference to the late Cenozoic molluscs of the Meade Basin, southwest Kansas.

Twenty-six fossil assemblages of land and freshwater molluscs from the Pliocene to the present, were collected from locations near the town of Meade, Kansas, U.S.A. and were analyzed (along with the extant molluscan fauna of Meade County, Kansas) to look for changes in molluscan diversity through time. The fossil assemblages were analyzed for two reasons: I) to test the hypothesis that diversity (measured as taxonomic richness, dominance, turnover and habitat type) did not change through the five million years of this study (HOI); and 2) to test the hypothesis that there is no relationship between the taxonomic composition of a molluscan assemblage and the local climate (H02)\u27 The latter hypothesis was tested by re-examining prior molluscan paleoecological studies, by analyzing the molluscan assemblages collected for this study and through ordination analysis. The results of the first analysis clearly showed that the taxonomic structure of the assemblages changed through time (HOI was falsified), but the changes appeared to be random fluctuations. Richness ranged from 7 taxa (in assemblages AGO, FAL, RYA, SPA) to 30 (C03B) with r2 = 0.237. Dominance ranged from 1.40 (SPA) to 9.66 (RTA) with r2 = 0.113. The Habitat Ratio ranged from -0.43 (FAL) to 1.00 (X I E) with r2 = 0.029 and Turnover ranged from 0.17 (AGO, F AL) to 1.00 (RNT), when each assemblage was compared to RNT (r2 = 0.024). No discernable long-tern trend in taxonomic diversity or community composition was observed. The results of the second analysis indicate that molluscs, as a group, are not as useful as climate indicators as previously supposed. Today, both land and freshwater mollusc species are broadly geographically distributed and thus are found in a variety of locations with different local climates and vegetation. Previously, Miller (1975, 1976) grouped molluscan species with similar environmental tolerances into four units called Climate Groups and used them to infer the past climatic conditions of a region. However, only a weak climate signal was detected (ANOY A found significant differences among the Groups for minimum temperature [p \u3c 0.0001], maximum temperature [p \u3c 0.0001] and annual precipitation [p = 0.0082]), after the previous results were reanalyzed using the methods of this study. The fossil molluscan assemblages collected for this study displayed no climate signal (ANOY A found no significant differences among the assemblages for minimum temperature [p = 0.0714] or precipitation [p =0.691] but did find a difference in maximum temperature [p = 0.0207]. A subsequent Tukey-Kramer HSD test failed to find significant differences among assemblages). Finally, the results from ordination analysis of my data did not show a strong relationship between the climate variables used in this study (minimum and maximum temperatures, annual precipitation) and the current geographic distribution of molluscan taxa. One should proceed with caution if molluscs are to be used to interpret climate. The results of this study do not provide a strong endorsement for using molluscs as paleoclimate indicators. This finding is counter to the prevailing wisdom among paleontologists. More work needs to be done in the area of molluscan biogeography and physiology to see if the conclusions herein hold up and to better understand molluscan biology in general

Hierarchical Clustering: O(1)-Approximation for Well-Clustered Graphs

Hierarchical clustering studies a recursive partition of a data set into clusters of successively smaller size, and is a fundamental problem in data analysis. In this work we study the cost function for hierarchical clustering introduced by Dasgupta, and present two polynomial-time approximation algorithms: Our first result is an $O(1)$-approximation algorithm for graphs of high conductance. Our simple construction bypasses complicated recursive routines of finding sparse cuts known in the literature. Our second and main result is an $O(1)$-approximation algorithm for a wide family of graphs that exhibit a well-defined structure of clusters. This result generalises the previous state-of-the-art, which holds only for graphs generated from stochastic models. The significance of our work is demonstrated by the empirical analysis on both synthetic and real-world data sets, on which our presented algorithm outperforms the previously proposed algorithm for graphs with a well-defined cluster structure.Comment: This work appeared at the 35th Conference on Neural Information Processing Systems (NeurIPS'21

Acts of the Apostles: edifying discourse or historical narrative

Intro. and Chapter 1. The reputation of Luke-Acts has varied greatiy. It has been acclaimed as a work of the highest historical value by some, and dismissed as tendentious and unreliable by others. Recent study has emphasised that the author was an original theologian, and has suggested that his theological concerns meant more to him than the recording of historical facts.Chapter 2. : J.C. O'Neill has claimed that Luke was a contemporary of Justin martyr, and the first of the Christian apologists. We dissent from this late dating, but find value in his comparison of Acts with Hellenistic Jewish missionary literature.Chapter 3. : The book of Acts is compared and contrasted with the books of Maccabees, the letter of Aristeas, and certain writings of Philo.The author, while holding to theological principles, is found to be concerned to present a record of fact.Chapter 4. : We consider traditions about the earliest church recorded in Acts 1-5» with conflict­ing estimates of their reliability. Adopting Erich Auerbach's distinction between saga and history, we conclude that the author has attempted to deal, as an historian, with material some of which reached him in the form of saga.Chapter 5 : The enigmatic figure of Stephen is studied, together with the Hellenists who appear in chapter 6. We conclude that Stephen was a real historical figure and that the speech in Acts 7 reflects something of his views.We consider attempts to link Stephen with the Samaritans and the community at Qumran.Chapter 6 : Paul is a key figure in Acts. Should the Paul of Acts be compared or contrasted with the Paul we meet in his letters? We argue , against Professor J. Knox, that Acts is a source of much reliable information about Paul, and that Acts and the Pauline letters are complementary to each other.Chapter 7 : Recent study has tended to the conclusion that the author of Acts had few, if any, written sources. We consider the 'Itinerary' theory - that he used a travel-document giving a list of Paul's stopping-place.Chapter 8 : We consider various forms of the 'Antiochsource' theory - that the author made use of a written record produced within the church at Antioch. It is argued that if written sources cannot be precisely identified, this does not mean that the author had none at all.Chapter 9 : The speeches of the books of Acts areconsidered. We discuss the attitude of ancient authors to the composition of speeches in historical writing. The speeche attributed to Peter and Paul are considered It is concluded that they do not simply represent the theological views of the author. He has used source material of various kinds to present the thoughts, if not the precise words, of the apostles.Chapter 10 : The speeches of the books of Acts areconsidered. We discuss the attitude of ancient authors to the composition of speeches in historical writing. The speeche attributed to Peter and Paul are considered It is concluded that they do not simply represent the theological views of the author. He has used source material of various kinds to present the thoughts, if not the precise words, of the apostles