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The New Foundations of Evolution: On the Tree of Life
... In botanical science, the concept of the autonomous individual has also been challenged by discoveries concerning rhizobia, mycorrhizae, and endocytic fungae. Nonetheless, zoologists long subscribed to a more individualist conception of the organism, since the role of microbial symbionts had been more difficult to document in animal evolution (Sapp 1994(Sapp , 2002(Sapp , 2009. We report here that the zoological sciences are also finding that animals are composites of many species living, developing, and evolving together. ...
... Still definitively demonstrating the symbiotic origin of eukaryotic organelles required the development of new molecular methods for showing evolutionary relationships in the microbial world. Methods based on comparisons of ribosomal RNA were developed by Carl Woese and colleagues, for exploring the hitherto unknown evolutionary relationships of microbes (see Sapp 2009). Those methods, when applied to mitochondria and chloroplast origins, revealed them to be relics of formerly free-living alphaproteobacteria and cyanobacteria, respectively. ...
... Today, molecular phylogeneticists generally agree that the nuclear genome of the mother cell, the engulfing host, was itself formed from the symbiotic fusion of an Archaean and one or perhaps two other lineages. The nature of those non-Archaean symbionts remains a subject of discussion among microbial phylogeneticists (Hartman and Federov 2002;Hall 2011; see also Sapp 2005Sapp , 2009. ...
The notion of the "biological individual" is crucial to studies of genetics, immunology, evolution, development, anatomy, and physiology. Each of these biological subdisciplines has a specific conception of individuality, which has historically provided conceptual contexts for integrating newly acquired data. During the past decade, nucleic acid analysis, especially genomic sequencing and high-throughput RNA techniques, has challenged each of these disciplinary definitions by finding significant interactions of animals and plants with symbiotic microorganisms that disrupt the boundaries that heretofore had characterized the biological individual. Animals cannot be considered individuals by anatomical or physiological criteria because a diversity of symbionts are both present and functional in completing metabolic pathways and serving other physiological functions. Similarly, these new studies have shown that animal development is incomplete without symbionts. Symbionts also constitute a second mode of genetic inheritance, providing selectable genetic variation for natural selection. The immune system also develops, in part, in dialogue with symbionts and thereby functions as a mechanism for integrating microbes into the animal-cell community. Recognizing the "holobiont"--the multicellular eukaryote plus its colonies of persistent symbionts--as a critically important unit of anatomy, development, physiology, immunology, and evolution opens up new investigative avenues and conceptually challenges the ways in which the biological subdisciplines have heretofore characterized living entities.
... Foundations of Evolution; On the Tree of Life, by Jan Sapp (2009). All unattributed page references are to quotations or information derived from this book. ...
... Theoretical adjustment proceeds more slowly than its technology; read Sapp (2009) to understand how contentious every step forward in microbiology had been, and how provisional each insight was in its time. The data were seldom ignored or dismissed, but always subject to reinterpretation. ...
Many readers of this journal have been schooled in both Darwinian evolution and Skinnerian psychology, which have in common the vision of powerful control of their subjects by their sequalae. Individuals of species that generate more successful offspring come to dominate their habitat; responses of those individuals that generate more reinforcers come to dominate the repertoire of the individual in that context. This is unarguable. What is questionable is how large a role these forces of selection play in the larger landscape of existing organisms and the repertoires of their individuals. Here it is argued that non-Darwinian and non-Skinnerian selection play much larger roles in both than the reader may appreciate. The argument is based on the history of, and recent advances in, microbiology. Lessons from that history re-illuminate the three putative domains of selection by consequences: The evolution of species, response repertoires, and cultures. It is argued that before, beneath, and after the cosmically brief but crucial epoch of Darwinian evolution that shaped creatures such as ourselves, non-Darwinian forces pervade all three domains.
... The identification of an unsuspected bifurcation among prokaryotes, the most abundant living organisms [29], immediately raised questions about the historical relationships between Archaea and Bacteria without nuclei, on the one hand, and Eukarya, the organisms with nucleated cells, on the other. Eukaryotes formed a coherent separate group based on ribosomal RNA sequences, and molecular phylogenies of different eukaryotic groups confirmed well---established taxonomic classifications, such as fungi, plants and animals. ...
... But the generic eukaryotic cell was closer to Bacteria in some features-membrane composition, metabolic pathways-and closer to Archaea in other features-replication, transcription and translation [30,31]. This phenotypic dichotomy gave support for longstanding but hotly disputed arguments championed by Lynn Margulis and others that symbiogenetic cell fusions served to create complex eukaryotic cells from simpler prokaryotic progenitors [29,[32][33][34][35][36]. ...
The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess "Read-Write Genomes" they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.
... These toxins have been reported to affect structural integrity of the coral tissue and results in extrusion of zooxanthallae from the normal location in the gastrodermis 31 . Experiments proved that lowest concentration of cyanobacterial toxin (Microcystin) promote bacterial growth in the coral tissue 32 and thus appearing to be directly toxic to corals. In the present study, occurrences of toxin producing stains such as Phormidium and Synechocystis within the BBD mat were found. ...
... The nucleotide sequences of 16S rRNA genes have been submitted to GenBank nucleotide sequence data base under accession numbers JF268250 to JF268255. Since late 1970s, the 16S rRNA gene based bacterial identification method has been used as a standard method for documentation of bacterial population in all habitats 32,33 and associationships including detection of the bacteria associated with WBD and BBD. ...
Black band disease (BBD) and white band diseases (WBD) are well-described diseases in corals worldwide and believed to be caused by a diverse microbial consortium. To expand our understanding of specific dominant bacterial community associated with the black band and white band diseased coral tissue, a culture-dependent approach was applied to diseased coral tissues of Acropora cytherea and Montipora digitata inhabiting Shingle Island of the Gulf of Mannar. Morphologically different dominant bacteria were isolated from corals affected with BBD and WBD for molecular identification. 16S rRNA gene sequence analysis revealed the dominance of isolates belongs to three genera Bacillus, Micrococcus, and vibrio in black band diseased Aropora cytheria. Moreover, two cyanobacterial species Phormidium sp. and Synechocystis sp also observed in diseased Aropora cytheria. In the case of white band disease in Montipora digitata, dominance of isolates belongs to three genera: Micrococcus, Psychrobacter and Palnomicrobium were found. The observed predominant bacterial candidate associated with BBD and WBD can be considered to find out the disease etiology.
... There are two kinds of augmented trees in XGBoost, regression trees, and classification trees. Optimizing the objective function of value is the core of XGBoost (Andersson, 2011;Hendrikx et al., 2014). ...
Ensemble learning algorithms show good forecasting performances for financial distress in many studies. Despite considering the feature selection and feature importance procedures, most overlook imbalanced data handling. This study proposes the Easyensemble method based on undersampling and combines it with ensemble learning models to predict financial distress. The results show that Easyensemble sampling presents better forecasting performance than SMOTE sampling. We subsequently conduct Permutation Importance (PIMP), Recursive Feature Elimination (RFE), and partial dependence plots, and the experimental results show that the feature selection procedure can effectively reduce the number of indicators without affecting the prediction accuracy, improve the prediction efficiency as well as save processing time. In addition, the indicators from profitability, cash flow, solvency, and structural ratios are essential in predicting financial distress.
... Through the second-order Taylor approximation of the objective function, the greedy algorithm is used to search for the segmentation point with the highest score, and the next step is to segment and expand the leaf nodes. This has the advantage of ensuring that the tree structure will not be too complicated and over-fitted in the process of minimizing the loss function, on the other hand, improving the computational efficiency [9][10]. ...
Stock price prediction has always been a hot issue in the financial sector and quantitative investment. Since stock price time series data tends to have linear and nonlinear features, traditional ARIMA models exhibit certain limitations in modeling such data. Based on this, this paper innovatively uses intraday transaction data of the stock market as auxiliary information, and proposes an improved ARIMA stock price prediction model based on machine learning methods. The specific principle is to use the ARIMA model to predict the linear information of the data, and machine learning-related algorithms (RF, XGBoost, LSTM) are used to predict the nonlinear residual information. The empirical results show that compared with the traditional ARIMA model, the model can effectively improve the prediction accuracy and is robust in stock price prediction. Finally, because this framework is very flexible in content, it can be equipped with machine learning methods with the best prediction accuracy for different practical application scenarios. In addition, we can use the model averaging method in the two-stage framework to improve the accuracy, and the mixed or high-frequency data can be further mined.
... Yet in the last 15 years biologists and philosophers of biology have regularly questioned the genuinely unifying character of this Synthesis, as well as its explanatory accuracy [11]. Those criticisms questioned notably the set of objects privileged by the Modern Synthesis, arguably too gene-centered [12], and its key explanatory processes, since niche construction [13], lateral gene transfer [14,15], phenotypic plasticity [16,17], and mass extinction [18] could, for example, be added [11]. Usually these critiques emphasize aspects rooted in a particular biological discipline: lateral gene transfer from microbiology, plasticity from developmental biology, mass extinction from paleobiology, ecosystem engineering from functional ecology, etc. ...
The classic Darwinian theory and the Synthetic evolutionary theory and their linear models, while invaluable to study the origins and evolution of species, are not primarily designed to model the evolution of organisations, typically that of ecosystems, nor that of processes. How could evolutionary theory better explain the evolution of biological complexity and diversity? Inclusive network-based analyses of dynamic systems could retrace interactions between (related or unrelated) components. This theoretical shift from a Tree of Life to a Dynamic Interaction Network of Life, which is supported by diverse molecular, cellular, microbiological, organismal, ecological and evolutionary studies, would further unify evolutionary biology.
... Greenhouse world therefore demonstrates how diverse com- munities can scale down to a stable state, whereas in Exo- Gaia we seed with a single species, and the microbe commu- nity must evolve suitable metabolisms to regulate their en- vironment, thus building up a regulating community where Greenhouse world reduces down. All life on Earth shares a common ancestor Sapp (2009), and so while it may theo- retically be possible for life to form independently multiple times, that does not seem to be the case on Earth, and so we mirror this behaviour in our model. ...
The search for habitable exoplanets inspires the question - how do habitable planets form? Planet habitability models traditionally focus on abiotic processes and neglect a biotic response to changing conditions on an inhabited planet. The Gaia hypothesis postulates that life influences the Earth's feedback mechanisms to form a self-regulating system, and hence that life can maintain habitable conditions on its host planet. If life has a strong influence, it will have a role in determining a planet's habitability over time. We present the ExoGaia model - a model of simple 'planets' host to evolving microbial biospheres. Microbes interact with their host planet via consumption and excretion of atmospheric chemicals. Model planets orbit a 'star' which provides incoming radiation, and atmospheric chemicals have either an albedo, or a heat-trapping property. Planetary temperatures can therefore be altered by microbes via their metabolisms. We seed multiple model planets with life while their atmospheres are still forming and find that the microbial biospheres are, under suitable conditions, generally able to prevent the host planets from reaching inhospitable temperatures, as would happen on a lifeless planet. We find that the underlying geochemistry plays a strong role in determining long-term habitability prospects of a planet. We find five distinct classes of model planets, including clear examples of 'Gaian bottlenecks' - a phenomenon whereby life either rapidly goes extinct leaving an inhospitable planet, or survives indefinitely maintaining planetary habitability. These results suggest that life might play a crucial role in determining the long-term habitability of planets.
... Greenhouse world therefore demonstrates how diverse com- munities can scale down to a stable state, whereas in Exo- Gaia we seed with a single species, and the microbe commu- nity must evolve suitable metabolisms to regulate their en- vironment, thus building up a regulating community where Greenhouse world reduces down. All life on Earth shares a common ancestor Sapp (2009), and so while it may theo- retically be possible for life to form independently multiple times, that does not seem to be the case on Earth, and so we mirror this behaviour in our model. ...
The search for habitable exoplanets inspires the question - how do habitable planets form? Planet habitability models traditionally focus on abiotic processes and neglect a biotic response to changing conditions on an inhabited planet. The Gaia hypothesis postulates that life influences the Earth’s feedback mechanisms to form a self-regulating system, and hence that life can maintain habitable conditions on its host planet. If life has a strong influence, it will have a role in determining a planet’s habitability over time. We present the ExoGaia model - a model of simple ‘planets’ host to evolving microbial biospheres. Microbes interact with their host planet via consumption and excretion of atmospheric chemicals. Model planets orbit a ‘star’ which provides incoming radiation, and atmospheric chemicals have either an albedo, or a heat-trapping property. Planetary temperatures can therefore be altered by microbes via their metabolisms. We seed multiple model planets with life while their atmospheres are still forming and find that the microbial biospheres are, under suitable conditions, generally able to prevent the host planets from reaching inhospitable temperatures, as would happen on a lifeless planet. We find that the underlying geochemistry plays a strong role in determining long-term habitability prospects of a planet. We find five distinct classes of model planets, including clear examples of ‘Gaian bottlenecks’ - a phenomenon whereby life either rapidly goes extinct leaving an inhospitable planet, or survives indefinitely maintaining planetary habitability. These results suggest that life might play a crucial role in determining the long-term habitability of planets.
... Evolutionary relatedness through molecular methods was quantifiable, and phylogenetics could reach deep into evolution's past. During the 1970s, Carl Woese and collaborators at the University of Illinois began to construct a universal tree of life based on comparisons of the small subunit ribosomal RNA which was conceived of as ''a universal chronometer'' at the core of the genetic machinery of all organisms (Sapp 2009). Their research led to the taxonomic proposal of three domains: Bacteria, Archaea and Eukarya, representing the three primary lineages of life (Woese et al. 1990). ...
The classical one genome-one organism conception of the individual is yielding today to a symbiotic conception of the organism. Microbial symbiosis is fundamental in our evolution, physiology and development. This notion, while not new, has been revitalized by advances in molecular methods for studying microbial diversity over the past decade. An ecological understanding of our microbial communities in health and disease supplements the venerable one germ-one disease conception of classical germ theory, and reinforces the view that nothing in biology makes sense except in light of symbiosis.
... The presence of a greater proportion of unclassified organisms in microbiomes of healthy subjects suggests that these individuals may host a greater proportion of nonpathogenic organisms than do autoimmune subjects. Historically, microbiology has focused on the characterization of microorganisms that cause disease, as well as their mechanisms of pathogenesis (de Kruif, 1926;Lechevalier and Solotorovsky, 1974;Sapp, 2009). Thus, if a bacterium is found that causes disease, the scientific community studies this organism immediately and with great intensity. ...
... The cited shortcomings in the New Synthesis (NS) are not recent. For decades already it has been argued that there is need for an upgraded or Extended New Synthesis (ENS, also abbreviated as EES by Laland et al., 2014) (Stebbins and Ayala 1981; Mayr 1993; De Loof 2002; Muller and Newman 2003; Pigliucci 2007; Heams et al. 2009; Sapp 2009; Pigliucci and Muller, 2011; Laland et al. 2014; Jablonka et al. 2014; Baluska 2011; Bauer 2012; Koonin 2012; Shapiro 2011 Shapiro , 2012 Pookottil 2013; Benneth 2014; Walsh 2015, and others), be it that not everybody is convinced that an upgrade should best be started from a new paradigm. Any emerging ENS should be compatible with an unambiguous definition of Life, it should take into account that living systems have two memory systems (genetic-and cognitive), and that cells have two major mechanisms of control of gene expression (coarse control by inorganic ions as well as fine tuning by, for instance, transcription factors). ...
Darwin’s theory of evolution with focus on the origin of new species was formulated in an era in which the principles of genetics, biochemistry, physiology, communication etc. were not an issue. Numerous revolutionary new insights have since been gained. 1. The ‘sender-receiver communicating compartment”, a classical but still valuable concept, is better suited than ‘the cell’ to serve the role of universal unit of structure and function, ‘the cell’ being the smallest such unit; 2. Not only genetic, but non-genetic mechanisms as well contribute to variability that can be passed onto the next generation; 3. Natural selection, the almost unanimously accepted universal driving force of evolution, is itself the result of preceding problem-solving activity enabled by the principles of communication; 4. A logically deduced, unambiguous definition of ‘Life’ has been published so that now the key question can shift from Darwin’s formulation towards “How does ‘Life’, with its many aspects, change in the course of time”? Communication activity represents the very heart of being alive, thus of ‘Life itself’. In digital-era wording, living entities are hardware-software double continua. This paper advances an easily teachable change in paradigm, namely that evolution concerns ever changing complexes of signalling pathways, chemical and other, that occasionally yield both new species and additional (at least 16) levels of communication. This approach complements the genetic basis of the New Synthesis with several as yet undervalued mechanisms from physiology and development. In particular, ‘the universal self-generated electrical dimension of cells’ and Lamarckism deserve an upgrade.
... 11 In this context, we need to investigate it, and consequently incorporate the concept of synergistic cooperation as one of the main scientific principles to explain the origin, organization and evolution of life in our planet. 11 Carrapiço, 2010b Carrapiço, , 2012 Corning, 2005; Margulis & Fester, 1991; Reid, 2007; Sapp, 2009; Sciama, 2013. ...
Beyond neo-Darwinism. Building a Symbiogenic Theory of Evolution
... 11 In this context, we need to investigate it, and consequently incorporate the concept of synergistic cooperation as one of the main scientific principles to explain the origin, organization and evolution of life in our planet. 11 Carrapiço, 2010b Carrapiço, , 2012 Corning, 2005; Margulis & Fester, 1991; Reid, 2007; Sapp, 2009; Sciama, 2013. ...
This short paper provides information on symbiosis and symbiogenesis, and reinforces the importance of these concepts in our understanding of the biological world and the role they play in the evolutionary complexity of living systems and in the establishing of the web of life in our planet. This will help to build a Symbiogenic Theory of Evolution and to introduce the new concept of symbiogenic superorganism. Este breve artigo fornece informações sobre simbiose e simbiogénese e reforça a importância desses conceitos para a compreensão do mundo natural e do papel que desempenham na complexidade evolutiva dos sistemas biológicos e no estabelecimento da "teia da vida" no nosso planeta. Todos estes dados contribuem para construir uma Teoria Simbiogénica da Evolução e introduzir o novo conceito de superorganismo simbiogénico. In order to understand a scientific theory, we should not only look
... However, the collection of vast amounts of gene sequence data has instead led to a realization of the frequency and prevalence of horizontal gene transfer and thus its centrality in the constitution of bacterial genomes. Rather than post-vital, this kind of meta-genomic work is a post-organismic vitalism, one that holds little regard for the individualization of life into discrete pieces, whether those pieces are individual bacteria or the species taxonomies humans built for bacteria in the late 19th and 20th centuries (Sapp, 2009; Helmreich, 2009). The scale of the material shift in the post-organismic, post-species bacterial pangenome – and the startling ubiquity of antibiotic resistance that it has produced – becomes comprehensible as the particular biology of modern history. ...
Beginning in the 1940s, mass production of antibiotics involved the industrial-scale growth of microorganisms to harvest their metabolic products. Unfortunately, the use of antibiotics selects for resistance at answering scale. The turn to the study of antibiotic resistance in microbiology and medicine is examined, focusing on the realization that individual therapies targeted at single pathogens in individual bodies are environmental events affecting bacterial evolution far beyond bodies. In turning to biological manifestations of antibiotic use, sciences fathom material outcomes of their own previous concepts. Archival work with stored soil and clinical samples produces a record described here as ‘the biology of history’: the physical registration of human history in bacterial life. This account thus foregrounds the importance of understanding both the materiality of history and the historicity of matter in theories and concepts of life today.
... " Indeed, there is a growing appreciation among biologists for the fact that symbiotic relationships are ubiquitous in nature and provide an important source of evolutionary innovations. (For more on symbiogenesis, seeSapp, 2004Sapp, , 2009Gontier, 2007;Carrapiço, 2010;Leigh, 2010aLeigh, , 2010bGilbert et al., 2012;Pereira et al., 2012.) A growing number of theorists over time have also explicitly adopted the term synergistic selection with regard to various biological phenomena. ...
Non-Darwinian theories of the emergence and evolution of complexity date back at least to Lamarck, and include those of Herbert Spencer and the “emergent evolution” theorists of the later nineteenth and early twentieth centuries. In recent decades, this approach has mostly been espoused by various practitioners in biophysics and complexity theory. However, there is a Darwinian alternative — in essence, an economic theory of complexity -- proposing that synergistic effects of various kinds have played an important causal role in the evolution of complexity, especially in the “major transitions.” We call this theory the “synergism hypothesis.” We posit that otherwise unattainable functional advantages arising from various cooperative phenomena have been favored over time in a dynamic that the late John Maynard Smith characterized and modeled as “synergistic selection.” The term highlights the fact that synergistic “wholes” may become interdependent “units” of selection. We provide some historical perspective on this issue, as well as a brief explication of the underlying theory and the concept of synergistic selection, and describe two relevant models.
... To make a comparative study of the six coding variants proposed in this work, two sets of nucleotide sequence data have been used. The first of them (termed 'Biodiversity dataset') includes sequences of SSU rRNA (the molecule considered as the best 'molecular clock' for phylogenetic studies since the pioneering work of Woese and Fox (1977; Sapp, 2009), of 32 organisms belonging to the three major groups or domains of cellular life: Archaea (18 sequences), Bacteria (8) and Eukarya (6). This set of data has been previously used to compare the phylogenetic reconstructions based on sequence data with those derived from functional information (Briones et al., 2005 ). ...
Motivation:
Self-organizing maps (SOMs) are readily available bioinformatics methods for clustering and visualizing high-dimensional data, provided that such biological information is previously transformed to fixed-size, metric-based vectors. To increase the usefulness of SOM-based approaches for the analysis of genomic sequence data, novel representation methods are required that automatically and objectively transform aligned nucleotide sequences into numeric vectors, dealing with both nucleotide ambiguity and gaps derived from sequence alignment.
Results:
Six different codification variants based on Euclidean space, just like SOM processing, have been tested using two SOM models: the classical Kohonen's SOM and growing cell structures. They have been applied to two different sets of sequences: 32 sequences of small sub-unit ribosomal RNA from organisms belonging to the three domains of life, and 44 sequences of the reverse transcriptase region of the pol gene of human immunodeficiency virus type 1 belonging to different groups and sub-types. Our results show that the most important factor affecting the accuracy of sequence clustering is the assignment of an extra weight to the presence of alignment-derived gaps. Although each of the codification variants shows a different level of taxonomic consistency, the results are in agreement with sequence-based phylogenetic reconstructions and anticipate a broad applicability of this codification method.
... Monera) and eukaryotic microbes (i.e. Protists), and then into three domains with the discovery of Archaea, in 1977 (reviewed in [1]). Starting in the mid-1980s, molecular systematic studies of rDNA sequences increased our knowledge of the biodiversity of Bacteria, microbial eukaryotes, and Archaea (the latter group having suffered a dearth of morphology-based studies [2]). ...
Microscopy has revealed tremendous diversity of bacterial and eukaryotic forms. Recent molecular analyses show discor-dance in estimates of biodiversity between morphological and molecular analyses. Moreover, phylogenetic analyses of the diversity of microbial forms reveal evidence of convergence at scales as deep as interdomain: morphologies shared between bacteria and eukaryotes. Here, we highlight examples of such discordance, focusing on exemplary lineages such as testate amoebae, ciliates, and cyanobacteria. These have long histories of morphological study, enabling deeper analyses on both the molecular and morphological sides. We discuss examples in two main categories: (i) morphologically identical (or highly similar) individuals that are genetically distinct and (ii) morphologically distinct individuals that are genetically the same. We argue that hypotheses about discordance can be tested using the concept of neutral morphologies, or more broadly neutral phenotypes, as a null hypothesis. Keywords: .mi crobial evolution; molecular data; morphology; neutral evolution "Thus, we have a neutral-morphology theory of evolution, where a variety of morphologies are equally successful in a particular environment. This makes an interesting contrast to the neutral-gene theory of Motoo Kimura. In the former, for one reason or another, natural selection fails to discriminate among phenotype morphologies, each of which has a distinctive genotype; in the latter, selection fails to discriminate among genotypes that all could have the same phenotype."
... The most common way for different species to share genetic information is via lateral gene transfer where genetic information is physically transferred from one organism to another pre-existing organism. Lateral gene transfer (LGT) had been conclusively shown in the 1940s to happen in the lab and it was known to be responsible for the spread of antibiotic resistance in the 1960s (Sapp 2009). But just how widespread in nature LGT was, was not known. ...
Phylogenetic trees are meant to represent the genealogical history of life and apparently derive their justification from the existence of the tree of life and the fact that evolutionary processes are treelike. However, there are a number of problems for these assumptions. Here it is argued that once we understand the important role that phylogenetic trees play as models that contain idealizations, we can accept these criticisms and deny the reality of the tree while justifying the continued use of trees in phylogenetic theory and preserving nearly all of what defenders of trees have called the “importance of tree thinking.”
... Inquilinism corresponds to another case of commensalism in which one organism lives within another, using the host as a refuge (Fraaye and Jäger, 1995). These symbioses are crucial factors in the evolution of the species (see Margulis, 1971Margulis, , 1998Margulis and Fester, 1991;Sapp, 1994Sapp, , 2009 producing various constraints for the partners that may or may not have been conserved through natural selection. Therefore, their study in the fossil record is particularly interesting. ...
... We propose that methods for defining homologous genes (gene families) that require homology to extend along most of the sequence (Miele et al. 2012) might be described by the search for " tribes " of proteins. We choose the word tribes, because this is the original meaning for the word phylogeny (from the Greek Phylos meaning " tribe " and Genis meaning " origin " ; Sapp 2009). Therefore, such tribes of sequences are likely to be amenable to phylogenetic tree or network construction using standard software currently available (Felsenstein 2004; Huson and Scornavacca 2011). ...
Defining homologous genes is important in many evolutionary studies but raises obvious issues. Some of these issues are conceptual, and stem from our assumptions of how a gene evolves, others are practical, and depend on the algorithmic decisions implemented in existing software. Therefore, in order to make progress in the study of homology, both ontological and epistemological questions must be considered. In particular, defining homologous genes cannot solely be addressed under the classic assumptions of strong tree-thinking, according to which genes evolve in a strictly tree-like fashion of vertical descent and divergence and the problems of homology detection are primarily methodological. Gene homology could also be considered under a different perspective where genes evolve as 'public goods', subjected to various introgressive processes. In this latter case, defining homologous genes becomes a matter of designing models suited to the actual complexity of the data and how such complexity arises, rather than trying to fit genetic data to some a priori tree-like evolutionary model, a practice that inevitably results in the loss of much information. Here we show how important aspects of the problems raised by homology detection methods can be overcome when even more fundamental roots of these problems are addressed by analysing 'public goods thinking' evolutionary processes through which genes have frequently originated. This kind of thinking acknowledges distinct types of homologs, characterised by distinct patterns, in phylogenetic and non phylogenetic unrooted or multi-rooted networks. In addition, we define "family resemblances" to include genes that are related through intermediate relatives, thereby placing notions of homology in the broader context of evolutionary relationships. We conclude by presenting some pay-offs of adopting such a pluralistic account of homology and family relationship, that expands the scope of evolutionary analyses beyond the traditional, yet relatively narrow focus allowed by a strong tree-thinking view on gene evolution.
... So who, if anyone, is actually defending the tree anymore? The most stalwart defence of the tree of life in recent years came not from biologists, but from a historian [100], and it could be that the most tree-prone among microbiologists would defend the method of using trees to study microbial evolution more vociferously than they might defend any particular tree itself [17]. As leaves and branches in the tree of life come and go, new approaches to the analysis of genome data will continue to emerge, some of which will be based neither on trees nor on networks [101]. ...
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.
... For a useful and self-contained introduction to the conventional, eukaryote-centric framework of evolutionary theory, accessible to physicists with little biological background, we refer the reader to the standard text by Maynard Smith[27]; an introduction that also covers physics-related topics especially has been given by Drossel[28] . Most of life is microbial, and a modern microbe-centric view of evolution can be found in the book by Sapp[29]. We envisage a readership with a wide range of knowledge and interest in evolutionary biology. ...
Evolution is the fundamental physical process that gives rise to biological phenomena. Yet it is widely treated as a subset of population genetics, and thus its scope is artificially limited. As a result, the key issues of how rapidly evolution occurs, and its coupling to ecology have not been satisfactorily addressed and formulated. The lack of widespread appreciation for, and understanding of, the evolutionary process has arguably retarded the development of biology as a science, with disastrous consequences for its applications to medicine, ecology and the global environment. This review focuses on evolution as a problem in non-equilibrium statistical mechanics, where the key dynamical modes are collective, as evidenced by the plethora of mobile genetic elements whose role in shaping evolution has been revealed by modern genomic surveys. We discuss how condensed matter physics concepts might provide a useful perspective in evolutionary biology, the conceptual failings of the modern evolutionary synthesis, the open-ended growth of complexity, and the quintessentially self-referential nature of evolutionary dynamics. Comment: To appear in Annual Reviews of Condensed Matter Physics (2011)
... The presence of a greater proportion of unclassified organisms in microbiomes of healthy subjects suggests that these individuals may host a greater proportion of nonpathogenic organisms than do autoimmune subjects. Historically, microbiology has focused on the characterization of microorganisms that cause disease , as well as their mechanisms of pathogenesis (de Kruif, 1926; Lechevalier and Solotorovsky, 1974; Sapp, 2009). Thus, if a bacterium is found that causes disease, the scientific community studies this organism immediately and with great intensity. ...
Several studies have shown that gut bacteria have a role in diabetes in murine models. Specific bacteria have been correlated with the onset of diabetes in a rat model. However, it is unknown whether human intestinal microbes have a role in the development of autoimmunity that often leads to type 1 diabetes (T1D), an autoimmune disorder in which insulin-secreting pancreatic islet cells are destroyed. High-throughput, culture-independent approaches identified bacteria that correlate with the development of T1D-associated autoimmunity in young children who are at high genetic risk for this disorder. The level of bacterial diversity diminishes overtime in these autoimmune subjects relative to that of age-matched, genotype-matched, nonautoimmune individuals. A single species, Bacteroides ovatus, comprised nearly 24% of the total increase in the phylum Bacteroidetes in cases compared with controls. Conversely, another species in controls, represented by the human firmicute strain CO19, represented nearly 20% of the increase in Firmicutes compared with cases overtime. Three lines of evidence are presented that support the notion that, as healthy infants approach the toddler stage, their microbiomes become healthier and more stable, whereas, children who are destined for autoimmunity develop a microbiome that is less diverse and stable. Hence, the autoimmune microbiome for T1D may be distinctly different from that found in healthy children. These data also suggest bacterial markers for the early diagnosis of T1D. In addition, bacteria that negatively correlated with the autoimmune state may prove to be useful in the prevention of autoimmunity development in high-risk children.
After a brief prologue on Otto Kandler’s life, we describe briefly his pioneering work on photosynthesis (photophosphorylation and the carbon cycle) and his key participation in the discovery of the concept of three forms of life (Archaea, Prokarya, and Eukarya). With Otto Kandler’s passing, both the international photosynthesis and microbiology communities have lost an internationally unique, eminent, and respected researcher and teacher who exhibited a rare vibrancy and style.
This paper explores the case of using robots to simulate evolution, in particular the case of Hamilton’s Law. The uses of robots raises several questions that this paper seeks to address. The first concerns the role of the robots in biological research: do they simulate something (life, evolution, sociality) or do they participate in something? The second question concerns the physicality of the robots: what difference does embodiment make to the role of the robot in these experiments. Thirdly, how do life, embodiment and social behavior relate in contemporary biology and why is it possible for robots to illuminate this relation? These questions are provoked by a strange similarity that has not been noted before: between the problem of simulation in philosophy of science, and Deleuze’s reading of Plato on the relationship of ideas, copies and simulacra.
The paper develops a performative account of the ways in which knowledge and space are co-produced as humans move, develop social networks, and extend their cognitive practices. Such an account enables alternative ways of conceiving what counts as knowledge and as modernity to be held in tension, thus allowing the emergent generative effects of the Argentinean philosopher Enrique Dussel's concept of 'transmodernity'. Working with differing knowledge traditions requires, as Walter Mignolo recommends, thinking " with, against and beyond the legacy of Western epistemology. " What is at issue is the capacity to move beyond the point of 'colonial difference' explored by Mignolo in which Western knowledge gets authorised as universal and the rest get classified as 'people without history'. Only then can we enable differing knowledge traditions to work together without subordinating them and absorbing their differences in the western panopticon. This is not an easy task since the Western knowledge tradition in the form of science is hegemonic, and all other traditions are rendered as incommensurable, but to commensurate them is by definition to subordinate them and rob them of their cultural specificity. Equally, simply seeing them as different interpretations or different world views is too weak in the struggle for authority. To flourish, to have autonomy in the face of hegemony, indigenous knowledge traditions have to have an effective voice and construct their own identities. What is offered in this paper is a performative framework which is strong enough to destabilise the hegemony of western epistemology and generative enough to allow for real difference and the growth of cultural diversity.
Reticulation is a recurring evolutionary pattern found in phylogenetic reconstructions of life. The pattern results from how species interact and evolve by mechanisms and processes including symbiosis; symbiogenesis; lateral gene transfer (that occurs via bacterial conjugation, transformation, transduction, Gene Transfer Agents, or the movements of transposons, retrotransposons, and other mobile genetic elements); hybridization or divergence with gene flow; and infectious heredity (induced either directly by bacteria, bacteriophages, viruses, prions, protozoa and fungi, or via vectors that transmit these pathogens). Research on reticulate evolution today takes on inter- and transdisciplinary proportions and is able to unite distinct research fields ranging from microbiology and molecular genetics to evolutionary biology and the biomedical sciences. This chapter summarizes the main principles of the diverse reticulate evolutionary mechanisms and situates them into the chapters that make up this volume.
Since the 1990s, results coming in from molecular phylogenetics necessitate us to recognize that Horizontal Gene Transfer (HGT) occurs massively across all three domains of life. Nonetheless, many of the mechanisms whereby genes can become transferred laterally have been known from the early twentieth century onward. The temporal discrepancy between the first historical observations of the processes, and the rather recent general acceptance of the documented data, poses an interesting epistemological conundrum: Why have incoming results on HGT been widely neglected by the general evolutionary community and what causes for a more favorable reception today? Five reasons are given: (1) HGT was first observed in the biomedical sciences and these sciences did not endorse an evolutionary epistemic stance because of the ontogeny/phylogeny divide adhered to by the founders of the Modern Synthesis. (2) Those who did entertain an evolutionary outlook associated research on HGT with a symbiotic epistemic framework. (3) That HGT occurs across all three domains of life was demonstrated by modern techniques developed in molecular biology, a field that itself awaits full integration into the general evolutionary synthesis. (4) Molecular phylogenetic studies of prokaryote evolution were originally associated with exobiology and abiogenesis, and both fields developed outside the framework provided by the Modern Synthesis. (5) Because HGT brings forth a pattern of reticulation, it contrasts the standard idea that evolution occurs solely by natural selection that brings forth a vertical, bifurcating pattern in the “tree” of life. Divided into two parts, this chapter first reviews current neo-Darwinian “tree of life” versus reticulate “web of life” polemics as they have been debated in high-profile academic journals, and secondly, the historical context of discovery of the various means whereby genes are transferred laterally is sketched. Along the way, the reader is introduced to how HGT contradicts some of the basic tenets of the neo-Darwinian paradigm.
This chapter introduces the important facets of the topic of producing phylogenetic trees, and the direct relevance to the study of infectious organisms' transmission. It is clearly important to be able to reconstruct the phylogeny, both for a group of species and also for the individuals within those species. Phylogenetics is based on the use of observable characteristics of contemporary organisms to try to deduce the sequence of events that occurred during the descent of those organisms. According to Charles Darwin, there are two distinct types of biological evolution—transformational evolution and variational evolution. Phylogenetic tree organizes our knowledge of biodiversity. It explains how closely organisms are related to each other. There are many other important uses of phylogenies including the study of co-phylogeny of hosts and pathogens. The term “pathogen” was coined around 1880, which was a time of great activity in the attempt to depict organismal relationships as trees. Reconstructing a phylogenetic history is conceptually straightforward. Phylogeneticists therefore feel confident that these phylogenetic methods also apply to situations where direct knowledge of the past is absent. Phylogenetic analysis of molecular sequences usually consists of three distinct procedures: sequence alignment, character coding, and tree building, which can be performed easily by choosing some popular computer programs and then using the default parameter values of those programs. There has been interest in the use of networks rather than trees as the basis for phylogenetic analysis.
The search for a universal tree of life, once considered outside the prevue of evolutionary biology, has led to a revolution in contemporary evolutionary biology while transcending its basic assumptions. Three primary lineages, the pervasiveness of horizontal gene transfer, and fundamental evolutionary role of symbiosis are at the center of microbial phylogenetic concepts today. Still, controversies remain. While many microbial phylogeneticists maintain that there is a small “core” of genes with “essential functions” that are refractory to HGT and through which one can determine the primary organismal lineages, others deny the existence of such a core and therefore the reality of organismal lineages at any taxonomic level.
The association of “two species that live on or in one another” was first described in the nineteenth century, and the word symbiosis was proposed to denote this biological phenomenon (Sapp 1994). The discovery that lichens are organisms generated by the integration of a fungus and blue-green algae, that is, cyanobacteria, was followed by a number of other studies that have shown how the association of different species is widespread in nature and characterized by different degrees of benefit-sharing. Symbiosis encompasses both antagonistic relationships, in which one organism takes advantage of the other, and mutualistic relationships, where both partners gain advantage from their association. There are also cases where no clear benefit or harm is evident for both interacting species, which are then, in some cases, considered commensals. The term symbiosis applies to all these type of species associations, and not only to mutualism, as is sometimes erroneously done (Sapp 1994).
As part of his attempt to reconstruct the earliest phase of the evolution of life on Earth, Woese produced a compelling critique of the received view of evolution from the 20th century. This paper explicitly articulates two related features of that critique that are fundamental but the first of which has not been sufficiently clearly recognized in the context of evolutionary theorizing: (1) according to Woese's scenario of communal evolution during life's earliest phase (roughly, the first billion years of life on Earth), well-defined biological individuals (and, thus, individual lineages) did not exist; and (2) during that phase, evolutionary change took place through ubiquitous horizontal gene transfer (HGT) rather than through vertical transmission of features (including genes) and the combinatorics of HGT was the dominant mechanism of evolutionary change. Both factors present serious challenges to the received view of evolution and that framework would have to be radically altered to incorporate these factors. The extent to which this will be necessary will depend on whether Woese's scenario of collective early evolution is correct.
Carl Woese developed a unique research program, based on rRNA, for discerning bacterial relationships and constructing a universal tree of life. Woese's interest in the evolution of the genetic code led to him to investigate the deep roots of evolution, develop the concept of the progenote, and conceive of the Archaea. In so doing, he and his colleagues at the University of Illinois in Urbana revolutionized microbiology and brought the classification of microbes into an evolutionary framework. Woese also provided definitive evidence for the role of symbiosis in the evolution of the eukaryotic cell while underscoring the importance of lateral gene transfer in microbial evolution. Woese and colleagues' proposal of three fundamental domains of life was brought forward in direct conflict with the prokaryote-eukaryote dichotomy. Together with several colleagues and associates, he brought together diverse evidence to support the rRNA evidence for the fundamentally tripartite nature of life. This paper aims to provide insight into his accomplishments, how he achieved them, and his place in the history of biology.
The paradox of widespread cooperation in an intensely competitive natural world has been a major focus of theory and research in evolutionary biology and related disciplines over the past several decades. While much of the earlier work in this vein was gene-centered and grounded in inclusive fitness (or kin selection) theory, more recent developments suggest that it might also be useful to view cooperation (and biological complexity) from a bioeconomic perspective. Here I will briefly explore the case for a paradigm shift, with special reference to the role of functional synergy as a distinct class of interdependent causal influences in evolution. I will argue that synergies of various kinds have been important drivers for cooperation in living systems at all levels. From this perspective, inclusive fitness and other factors may be enablers for cooperation, but the many exceptions show that genetic relatedness is neither necessary nor sufficient for the emergence of cooperative phenomena.
The pheneticist philosophy holds that biological taxa are clusters of entities united by a form of all-things-considered resemblance. This view of taxonomy has come in for almost universal criticism from philosophers, and has received little praise from biologists, over the past 30 years or so. This article defends a modest pheneticism, understood as part of a pluralist view of taxonomy. First, phenetic approaches to taxonomy are alive and well in biological practice, especially in the areas of microbiology and botany. Second, the pheneticist notion of overall similarity is defensible, and is implicitly endorsed even by those (such as Quine) usually implicated in attacks on similarity. Third, there are limited biological domains within which pheneticism’s conception of species as kinds (rather than heterogeneous individuals) remains applicable.
Studies of symbiosis by botanists in the nineteenth century were advanced in virtual conflict with the germ theory of disease,
and the emphasis on the struggle for existence in evolutionary biology. While many microbiologists focused on the pathogenic
effects of infectious germs in animals from the perspective of medicine, botanists examined the morphological and beneficial
effects of intimate microbe–plant relationships from an evolutionary perspective. Discussions of competing meanings of the
term “symbiosis” have included problems of anthropomorphisms on the one hand and difficulties in cost–benefit analysis on
the other.
The bulk of the diversity of eukaryotic life is microbial. Although the larger eukaryotes-namely plants, animals, and fungi-dominate our visual landscapes, microbial lineages compose the greater part of both genetic diversity and biomass, and contain many evolutionary innovations. Our understanding of the origin and diversification of eukaryotes has improved substantially with analyses of molecular data from diverse lineages. These data have provided insight into the nature of the genome of the last eukaryotic common ancestor (LECA). Yet, the origin of key eukaryotic features, namely the nucleus and cytoskeleton, remains poorly understood. In contrast, the past decades have seen considerable refinement in hypotheses on the major branching events in the evolution of eukaryotic diversity. New insights have also emerged, including evidence for the acquisition of mitochondria at the time of the origin of eukaryotes and data supporting the dynamic nature of genomes in LECA.
Ernst Mayr’s influence on philosophy of biology has given the field a particular perspective on evolution, phylogeny and life
in general. Using debates about the tree of life as a guide, I show how Mayrian evolutionary biology excludes numerous forms
of life and many important evolutionary processes. Hybridization and lateral gene transfer are two of these processes, and
they occur frequently, with important outcomes in all domains of life. Eukaryotes appear to have a more tree-like history
because successful lateral events tend to occur among more closely related species, or at a lower frequency, than in prokaryotes,
but this is a difference of degree rather than kind. Although the tree of life is especially problematic as a representation
of the evolutionary history of prokaryotes, it can function more generally as an illustration of the limitations of a standard
evolutionary perspective. Moreover, for philosophers, questions about the tree of life can be applied to the Mayrian inheritance
in philosophy of biology. These questions make clear that the dichotomy of life Mayr suggested is based on too narrow a perspective.
An alternative to this dichotomy is a multidimensional continuum in which different strategies of genetic exchange bestow
greater adaptiveness and evolvability on prokaryotes and eukaryotes.
KeywordsErnst Mayr-Philosophy of biology-Evolution-Tree of life-Species-Lateral gene transfer-Hybridization
In 1977, Carl Woese and George Fox published a brief paper in PNAS that established, for the first time, that the overall phylogenetic structure of the living world is tripartite. We describe the way in which this monumental discovery was made, its context within the historical development of evolutionary thought, and how it has impacted our understanding of the emergence of life and the characterization of the evolutionary process in its most general form.
Bacteria, pigs, rats, pots, plants, words, bones, stones, earrings, diseases, and genetic indicators of all varieties are markers and proxies for the complexity of interweaving trails and stories integral to understanding human movement and knowledge assemblage in Southeast Asia and around the world. Understanding human movement and knowledge assemblage is central to comprehending the genetic basis of disease, especially of a cancer like nasopharyngeal carcinoma. The problem is that the markers and trails, taken in isolation, do not all tell the same story. Human movement and knowledge assemblage are in constant interaction in an adaptive process of co-production with genes, terrain, climate, sea level changes, kinship relations, diet, materials, food and transport technologies, social and cognitive technologies, and knowledge strategies and transmission. Nasopharyngeal carcinoma is the outcome of an adaptive process involving physical, social, and genetic components.
The intent of this article is to provide a critical assessment of our current understanding of life's phylogenetic diversity. Phylogenetic comparison of gene sequences is a natural way to identify microorganisms and can also be used to infer the course of evolution. Three decades of molecular phylogenetic studies with various molecular markers have provided the outlines of a universal tree of life (ToL), the three-domain pattern of archaea, bacteria, and eucarya. The sequence-based perspective on microbial identification additionally opened the way to the identification of environmental microbes without the requirement for culture, particularly through analysis of rRNA gene sequences. Environmental rRNA sequences, which now far outnumber those from cultivars, expand our knowledge of the extent of microbial diversity and contribute increasingly heavily to the emerging ToL. Although the three-domain structure of the ToL is established, the deep phylogenetic structure of each of the domains remains murky and sometimes controversial. Obstacles to accurate inference of deep phylogenetic relationships are both systematic, in molecular phylogenetic calculations, and practical, due to a paucity of sequence representation for many groups of organisms.
Ernest Everett Just's critique of gene theory, his emphasis on the importance of cell cytoplasm, especially of the cortex in development and heredity, is placed within the context of his times, when the views of embryologists, who emphasized heredity as process, and those of geneticists who held determinist conceptions of the gene, were irreconcilable. Just's emphasis on the cell cortex in heredity and morphogenesis was appreciated by few, but was vindicated by studies of cortical inheritance and the morphogenetic role of pre-existing cell structure in ciliated protists. His essential criticisms of mechanism remain potent today.
Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms. There are now nearly 1,000 completed bacterial and archaeal genomes available, most of which were chosen for sequencing on the basis of their physiology. As a result, the perspective provided by the currently available genomes is limited by a highly biased phylogenetic distribution. To explore the value added by choosing microbial genomes for sequencing on the basis of their evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage. Analysis of these genomes demonstrated pronounced benefits (compared to an equivalent set of genomes randomly selected from the existing database) in diverse areas including the reconstruction of phylogenetic history, the discovery of new protein families and biological properties, and the prediction of functions for known genes from other organisms. Our results strongly support the need for systematic 'phylogenomic' efforts to compile a phylogeny-driven 'Genomic Encyclopedia of Bacteria and Archaea' in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come.
The concept of a tree of life is prevalent in the evolutionary literature. It stems from attempting to obtain a grand unified natural system that reflects a recurrent process of species and lineage splittings for all forms of life. Traditionally, the discipline of systematics operates in a similar hierarchy of bifurcating (sometimes multifurcating) categories. The assumption of a universal tree of life hinges upon the process of evolution being tree-like throughout all forms of life and all of biological time. In multicellular eukaryotes, the molecular mechanisms and species-level population genetics of variation do indeed mainly cause a tree-like structure over time. In prokaryotes, they do not. Prokaryotic evolution and the tree of life are two different things, and we need to treat them as such, rather than extrapolating from macroscopic life to prokaryotes. In the following we will consider this circumstance from philosophical, scientific, and epistemological perspectives, surmising that phylogeny opted for a single model as a holdover from the Modern Synthesis of evolution.
It was far easier to envision and defend the concept of a universal tree of life before we had data from genomes. But the belief that prokaryotes are related by such a tree has now become stronger than the data to support it. The monistic concept of a single universal tree of life appears, in the face of genome data, increasingly obsolete. This traditional model to describe evolution is no longer the most scientifically productive position to hold, because of the plurality of evolutionary patterns and mechanisms involved. Forcing a single bifurcating scheme onto prokaryotic evolution disregards the non-tree-like nature of natural variation among prokaryotes and accounts for only a minority of observations from genomes.
Prokaryotic evolution and the tree of life are two different things. Hence we will briefly set out alternative models to the tree of life to study their evolution. Ultimately, the plurality of evolutionary patterns and mechanisms involved, such as the discontinuity of the process of evolution across the prokaryote-eukaryote divide, summons forth a pluralistic approach to studying evolution.
This article was reviewed by Ford Doolittle, John Logsdon and Nicolas Galtier.
Two significant evolutionary processes are fundamentally not tree-like in nature--lateral gene transfer among prokaryotes and endosymbiotic gene transfer (from organelles) among eukaryotes. To incorporate such processes into the bigger picture of early evolution, biologists need to depart from the preconceived notion that all genomes are related by a single bifurcating tree.