Tree-like Process Research Articles

The Net of Life, a short story: Intricate patterns of gene flows across hundreds of extant genomes, all the way to LUCA

Over the past quarter-century, the field of evolutionary biology has been transformed by the emergence of complete genome sequences and the conceptual framework known as the 'Net of Life.' This paradigm shift challenges traditional notions of evolution as a tree-like process, emphasizing the complex, interconnected network of gene flow that may blur the boundaries between distinct lineages. In this context, gene loss, rather than horizontal gene transfer, is the primary driver of gene content, with vertical inheritance playing a principal role. The 'Net of Life' not only impacts our understanding of genome evolution but also has profound implications for classification systems, the rapid appearance of new traits, and the spread of diseases. Here, we explore the core tenets of the 'Net of Life' and its implications for genome-scale phylogenetic divergence, providing a comprehensive framework for further investigations in evolutionary biology.

Due date assignment and dynamic scheduling of one-of-a-kind assembly production with uncertain processing time

In this paper, dynamic scheduling and due date assignment of one-of-a-kind assembly production is studied when the processing time is uncertain and normally distributed. New product arrives randomly with exponentially distributed inter-arrival times. Each product has its unique tree-like process route. To solve this problem, first, a method is proposed to calculate the probability that a product can be completed before its due date. Based on this method, start times of cross-points are optimised to obtain the largest in-time completion probability (ITCP). Second, two new combined dispatch rules are constructed by considering critical path (CP), the latest start time of operation and the impact from newly arrived products. Lastly, a binary search-based due date assignment method is proposed, which assigns a relative early due date to every product and meanwhile guarantee its probability of being completed before the due date. Results of numerical experiments indicate that two proposed rules are more effective in increasing the ITCP than other dispatch rules such as the first-come-first-service rule and the shortest processing time rule, and also indicate that the binary search-based due date assignment method can assign relatively early due date to newly arrived products than other due date assignment methods.

Phylo SI: a new genome-wide approach for prokaryotic phylogeny

The evolutionary history of all life forms is usually represented as a vertical tree-like process. In prokaryotes, however, the vertical signal is partly obscured by the massive influence of horizontal gene transfer (HGT). The HGT creates widespread discordance between evolutionary histories of different genes as genomes become mosaics of gene histories. Thus, the Tree of Life (TOL) has been questioned as an appropriate representation of the evolution of prokaryotes. Nevertheless a common hypothesis is that prokaryotic evolution is primarily tree-like, and a routine effort is made to place new isolates in their appropriate location in the TOL. Moreover, it appears desirable to exploit non–tree-like evolutionary processes for the task of microbial classification. In this work, we present a novel technique that builds on the straightforward observation that gene order conservation (‘synteny’) decreases in time as a result of gene mobility. This is particularly true in prokaryotes, mainly due to HGT. Using a ‘synteny index’ (SI) that measures the average synteny between a pair of genomes, we developed the phylogenetic reconstruction tool ‘Phylo SI’. Phylo SI offers several attractive properties such as easy bootstrapping, high sensitivity in cases where phylogenetic signal is weak and computational efficiency. Phylo SI was tested both on simulated data and on two bacterial data sets and compared with two well-established phylogenetic methods. Phylo SI is particularly efficient on short evolutionary distances where synteny footprints remain detectable, whereas the nucleotide substitution signal is too weak for reliable sequence-based phylogenetic reconstruction. The method is publicly available at http://research.haifa.ac.il/ssagi/software/PhyloSI.zip.

An Efficient Dispatching Rule in One-of-a-Kind Assembly Production

In this paper, we researched a one-of-a-kind assembly production system where every product is unique (i.e. each product has its unique tree-like process route) and arrives one by one randomly with the exponentially distributed inter arrival times. We proposed a new effective combined dispatching rule (LFD/RPS/CP rule) that is constructed by considering three factors: the latest finishing date (LFD), the remaining path size (RPS) and whether an operation is on the critical path (CP). We did many numerical experiments to compare the efficiency between the proposed rule and other rules that were reported in existing studies such as LFD rule and EDD rule. The performance analysis shows that the proposed dispatching rule is more effective in reducing the number of tardy products and total tardiness time.

An Efficient Dispatching Rule in One-of-a-Kind Assembly Production

In this paper, we researched a one-of-a-kind assembly production system where every product is unique (i.e. each product has its unique tree-like process route) and arrives one by one randomly with the exponentially distributed inter arrival times. We proposed a new effective combined dispatching rule (LFD/RPS/CP rule) that is constructed by considering three factors: the latest finishing date (LFD), the remaining path size (RPS) and whether an operation is on the critical path (CP). We did many numerical experiments to compare the efficiency between the proposed rule and other rules that were reported in existing studies such as LFD rule and EDD rule. The performance analysis shows that the proposed dispatching rule is more effective in reducing the number of tardy products and total tardiness time.

A New Combined Dispatching Rule of One-of-a-Kind Assembly Production Process

In this paper, we researched a one-of-a-kind assembly production system where every product is unique (i.e. each product has its unique tree-like process route) and arrives one by one randomly with the exponentially distributed interarrival times. We proposed a new effective combined dispatching rule (ELFT rule) that is constructed by considering three factors: the latest finishing time (LFT), the remaining path size (RPS) and whether an operation is on the critical path (CP). We did many numerical experiments to compare the efficiency between the proposed rule and other rules that were reported in existing studies such as LFT rule and EDD rule. The performance analysis shows that the proposed dispatching rule is more effective in reducing the number of tardy products and total tardiness time.

Early evolution without a tree of life

Life is a chemical reaction. Three major transitions in early evolution are considered without recourse to a tree of life. The origin of prokaryotes required a steady supply of energy and electrons, probably in the form of molecular hydrogen stemming from serpentinization. Microbial genome evolution is not a treelike process because of lateral gene transfer and the endosymbiotic origins of organelles. The lack of true intermediates in the prokaryote-to-eukaryote transition has a bioenergetic cause.This article was reviewed by Dan Graur, W. Ford Doolittle, Eugene V. Koonin and Christophe Malaterre.

Genome Networks Root the Tree of Life between Prokaryotic Domains

Eukaryotes arose from prokaryotes, hence the root in the tree of life resides among the prokaryotic domains. The position of the root is still debated, although pinpointing it would aid our understanding of the early evolution of life. Because prokaryote evolution was long viewed as a tree-like process of lineage bifurcations, efforts to identify the most ancient microbial lineage split have traditionally focused on positioning a root on a phylogenetic tree constructed from one or several genes. Such studies have delivered widely conflicting results on the position of the root, this being mainly due to methodological problems inherent to deep gene phylogeny and the workings of lateral gene transfer among prokaryotes over evolutionary time. Here, we report the position of the root determined with whole genome data using network-based procedures that take into account both gene presence or absence and the level of sequence similarity among all individual gene families that are shared across genomes. On the basis of 562,321 protein-coding gene families distributed across 191 genomes, we find that the deepest divide in the prokaryotic world is interdomain, that is, separating the archaebacteria from the eubacteria. This result resonates with some older views but conflicts with the results of most studies over the last decade that have addressed the issue. In particular, several studies have suggested that the molecular distinctness of archaebacteria is not evidence for their antiquity relative to eubacteria but instead stems from some kind of inherently elevated rate of archaebacterial sequence change. Here, we specifically test for such a rate elevation across all prokaryotic lineages through the analysis of all possible quartets among eight genes duplicated in all prokaryotes, hence the last common ancestor thereof. The results show that neither the archaebacteria as a group nor the eubacteria as a group harbor evidence for elevated evolutionary rates in the sampled genes, either in the recent evolutionary past or in their common ancestor. The interdomain prokaryotic position of the root is thus not attributable to lineage-specific rate variation.

Molecular phylogeny: reconstructing the forest

Phylogeny, be it morphological or molecular, has long tried to explain the extant biodiversity by the Tree of Species, which is a logical consequence of strict Darwinian evolutionary principles. Through constant improvement of both methods and data sets, some parts of this diversity have actually been demonstrated to be the result of a tree-like process. For some other parts, and especially for prokaryotes, different molecular markers have, however, produced different evolutionary trees, preventing the reconstruction of such a Tree. While technical artifacts could be blamed for these discrepancies, Lateral Gene Transfers are now largely held for responsible, and their existence requires an extension of the Darwinian framework, since genetic material is not always vertically inherited from parents to offspring. Through a variety of biological processes, sometimes large parts of DNA are exchanged between phylogenetically distant contemporary organisms, especially between those sharing the same environment. While mainly concerning prokaryotes, Lateral Gene Transfers have been also demonstrated to affect eukaryotes, and even multicellular ones, like plants or animals. Most of the time, these transfers allow important adaptations and the colonisation of new niches. The quantitative and qualitative importance of genetic transfers has thus severely challenged the very existence of a universal Tree of Species, since genetic connections, at least for microbes, seem more reticulated than tree-like. Even traditional biological concepts, like the concept of species, need to be re-evaluated in the light of recent discoveries. In short, instead of focusing on a elusive universal tree, biologists are now considering the whole forest corresponding to the multiple processes of inheritance, both vertical and horizontal. This constitutes the major challenge of evolutionary biology for the years to come. To cite this article: P. Lopez, E. Bapteste, C. R. Biologies 332 (2009).

Genome history in the symbiotic hybrid Euglena gracilis

Euglena gracilis has a chimeric gene collection in which some genes were inherited from its heterotrophic host and others were acquired from a photoautotrophic endosymbiont during secondary endosymbiosis. The evolutionary reconstruction of such a hybrid genome poses a challenge for standard phylogenetic tools that produce bifurcating trees because genome evolution by endosymbiotic gene transfer is a non tree-like process. We sequenced 2770 ESTs from E. gracilis, of which 841 have homologues in a sample of other eukaryotes. Most of these homologues are found in all of the eukaryotes in our sample, but 117 of them are specific to photoautotrophic eukaryotes. A phylogenetic tree fails to account for this observation but the distribution of homologues and a phylogenetic network clearly show the common origin of E. gracilis from both kinetoplastid and photoautotrophic ancestors.

Analyzing priority queues with 3 classes using tree-like processes

In this paper we demonstrate how tree-like processes can be used to analyze a general class of priority queues with three service classes, creating a new methodology to study priority queues. The key result is that the operation of a 3-class priority queue can be mimicked by means of an alternate system that is composed of a single stack and queue. The evolution of this alternate system is reduced to a tree-like Markov process, the solution of which is realized through matrix analytic methods. The main performance measures, i.e., the queue length distributions and loss rates, are obtained from the steady state of the tree-like process through a censoring argument. The strength of our approach is demonstrated via a series of numerical examples.

Transient analysis of tree-Like processes and its application to random access systems

A new methodology to assess transient performance measures of tree-like processes is proposed by introducing the concept of tree-like processes with marked time epochs. As opposed to the standard tree-like process, such a process marks part of the time epochs by following a set of Markovian rules. Our interest lies in obtaining the system state at the n -th marked time epoch as well as the mean time at which this n -th marking occurs. The methodology transforms the transient problem into a stationary one by applying a discrete Erlangization and constructing a reset Markov chain. A fast algorithm, with limited memory usage, that exploits the block structure of the reset Markov chain is developed and is based, among others, on Sylvester matrix equations and fast Fourier transforms. The theory of tree-like processes generalizes the well-known paradigm of Quasi-Birth-Death Markov chains and has various applications. We demonstrate our approach on the celebrated Capetanakis-Tsybakov-Mikhailov (CTM) random access protocol yielding new insights on its initial behavior both in normal and overload conditions.

Linking priority queues and tree-like processes

This paper links the analysis of a general class of priority queues with three service classes with tree-like processes. This is realized by demonstrating that the operation of a 3-class priority queue can be mimicked by means of an alternate system that is composed of a single stack and queue. Some insights on how to reduce the evolution of this alternate system to a tree-like process are provided, allowing an efficient solution of the priority system through matrix analytic methods.

A GROWING NETWORK OF IDEAS

The term "self-organized criticality" in the scientific literature is shown to have spread in a fractal, tree-like process. The probability that one of the original papers will be cited in a subsequent paper is related to the random network growth of the entire field, much like the growth of the World Wide Web. This is in opposition to recent publications that argue for a multiplicative process in scientific publishing where publishing success is based on attributes directly inherent to the author.

Expected Utility and Sequential Elimination Models of Career Decision Making

Participants selected careers following three decision-making models: (a) an Expected Utility model in which participants rated the importance of work values and the subjective probabilities associated with each of these values being satisfied within various occupations, (b) a Sequential Elimination model in which participants selected a career following an individually tailored tree-like process based on the successive elimination of career options, and (c) an unspecified model in which participants′ selections were unguided by an explicit model. Comparisons of the quality of the career decisions made under each of the three models were evaluated in terms of: (a) the quality of choices relative to the "ideal" career selected in the Expected Utility model, (b) the types of career selected, and (c) postdecisional satisfaction. The results suggested that the Expected Utility model yielded the highest payoff (expected utility) of the three approaches, but that the Sequential Elimination and unspecified models did not differ from each other in the expected utilities of their top careers. Additionally, the Expected Utility model differed significantly from the Sequential Elimination model and the unspecified model in terms of the frequencies with which different types of careers were selected, but no such differences were identified between the other two models. No difference was found between the Sequential Elimination and the unspecified model in terms of postdecisional satisfaction.