A Place for Viruses on the Tree of Life

Viruses are ubiquitous. They infect almost every species and are probably the most abundant biological entities on the planet, yet they are excluded from the Tree of Life (ToL). However, there can be no doubt that viruses play a significant role in evolution, the force that facilitates all life on Earth. Conceptually, viruses are regarded by many as non-living entities that hijack living cells in order to propagate. A strict separation between living and non-living entities places viruses far from the ToL, but this may be theoretically unsound. Advances in sequencing technology and comparative genomics have expanded our understanding of the evolutionary relationships between viruses and cellular organisms. Genomic and metagenomic data have revealed that co-evolution between viral and cellular genomes involves frequent horizontal gene transfer and the occasional co-option of novel functions over evolutionary time. From the giant, ameba-infecting marine viruses to the tiny Porcine circovirus harboring only two genes, viruses and their cellular hosts are ecologically and evolutionarily intertwined. When deciding how, if, and where viruses should be placed on the ToL, we should remember that the Tree functions best as a model of biological evolution on Earth, and it is important that models themselves evolve with our increasing understanding of biological systems.

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Comparison of fundamental physical properties of the model cells (protocells) and the living cells reveals the need in protophysiology

International Journal of Astrobiology ◽

10.1017/s1473550415000476 ◽

2016 ◽

Vol 16 (1) ◽

pp. 97-104 ◽

Cited By ~ 7

Author(s):

V.V. Matveev

Keyword(s):

Physical Properties ◽

Origin Of Life ◽

Sodium Pump ◽

Molecular Model ◽

Biological Evolution ◽

Living Cells ◽

Real Problem ◽

The Origin Of Life ◽

Physical Laws ◽

Fundamental Physical

AbstractA hypothesis is proposed about potassium ponds being the cradles of life enriches the gamut of ideas about the possible conditions of pre-biological evolution on the primeval Earth, but does not bring us closer to solving the real problem of the origin of life. The gist of the matter lies in the mechanism of making a delimitation between two environments – the intracellular environment and the habitat of protocells. Since the sodium–potassium pump (Na+/K+-ATPase) was discovered, no molecular model has been proposed for a predecessor of the modern sodium pump. This has brought into life the idea of the potassium pond, wherein protocells would not need a sodium pump. However, current notions of the operation of living cells come into conflict with even physical laws when trying to use them to explain the origin and functioning of protocells. Thus, habitual explanations of the physical properties of living cells have become inapplicable to explain the corresponding properties of Sidney Fox's microspheres. Likewise, existing approaches to solving the problem of the origin of life do not see the need for the comparative study of living cells and cell models, assemblies of biological and artificial small molecules and macromolecules under physical conditions conducive to the origin of life. The time has come to conduct comprehensive research into the fundamental physical properties of protocells and create a new discipline – protocell physiology or protophysiology – which should bring us much closer to solving the problem of the origin of life.

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A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

10.1101/2021.02.22.431589 ◽

2021 ◽

Author(s):

William J. Baker ◽

Paul Bailey ◽

Vanessa Barber ◽

Abigail Barker ◽

Sidonie Bellot ◽

...

Keyword(s):

Natural History ◽

Flowering Plants ◽

Tree Of Life ◽

Flowering Plant ◽

Target Sequence ◽

Sequence Capture ◽

Natural History Collections ◽

Public Data ◽

Data Release ◽

Life On Earth

AbstractThe tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. This paper (i) documents our methods, (ii) describes our first data release and (iii) presents a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic dataset for angiosperms to date, comprising 3,099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%) and 2,333 genera (17%). Using the multi-species coalescent, we inferred a “first pass” angiosperm tree of life from the data, which totalled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns. The tree is strongly supported and highly congruent with existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated dataset, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer. This major milestone towards a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardised nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections.

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Teaching biological evolution - internal and external evaluation of learning outcomes

Nordic Studies in Science Education ◽

10.5617/nordina.349 ◽

2012 ◽

Vol 5 (2) ◽

pp. 171-184

Author(s):

Clas Olander

Keyword(s):

Biological Evolution ◽

National Sample ◽

External Evaluation ◽

Process Data ◽

Theory Of Evolution ◽

Before And After ◽

Teaching Learning ◽

Life On Earth ◽

Evaluation Of Learning ◽

Experimental Group

This paper reports from a study where teachers and researchers collaborate on designing and validatingtopic-oriented teaching-learning sequences. In an iterative process, data about learning andteaching biological evolution are generated through continuous cycles of design, teaching, evaluation,and redesign. The study involved 180 Swedish students aged 11 – 16, and the overall learning aim was that the students should be able to use the theory of evolution as a tool when explaining the development of life on earth. The aim of this paper is to validate the students’ learning outcome, estimated as appropriation of scientific ways of reasoning in written answers. The students’ answers of questions are analysed before and after interventions (internal evaluation), and compared with the answers from a national sample (external evaluation). The students in the experimental group did develop their reasoning, and they attained the aim, to a greater extent than a national sample.

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Islamic Theological Views on Darwinian Evolution

Oxford Research Encyclopedia of Religion ◽

10.1093/acrefore/9780199340378.013.36 ◽

2016 ◽

Cited By ~ 2

Author(s):

Nidhal Guessoum

Keyword(s):

Evolutionary Process ◽

Darwinian Evolution ◽

Theory Of Evolution ◽

Human Exceptionalism ◽

The World ◽

The Problem Of Evil ◽

History Of ◽

Life On Earth ◽

Biological Entities ◽

Muslim Scholars

The various positions that Muslim scholars have adopted vis-à-vis Darwin’s theory of evolution since its inception in 1859 are here reviewed with an eye on the theological arguments that are embraced, whether explicitly or implicitly. A large spectrum of views and arguments are thus found, ranging from total rejection to total acceptance, including “human exceptionalism” (evolution is applicable to all organisms and animals but not to humans). The two main theological arguments that are thus extracted from Muslim scholars’ discussions of evolution are: 1) Is God excluded by the evolutionary paradigm or does the term “Creator” acquire a new definition? 2) Does Adam still exist in the human evolution scenario, and how to include his Qur’anic story in the scientific scenario? Additional, but less crucial issues are sometimes raised in Islamic discussions of evolution: a) Does the extinction of innumerable species during the history of life on earth conflict with the traditional view of God’s creation? b) Is theodicy (“the problem of evil”) exacerbated or explained by evolution? c) Are “species” well-defined and important biological entities in the Islamic worldview? d) Can the randomness that seems inherent in the evolutionary process be reconciled with a divine creation plan? These questions are here reviewed through the writings and arguments of Muslim scholars, and general conclusions are drawn about why rejectionists find it impossible to address those issues in a manner that is consistent with their religious principles and methods, and why more progressive, less literalistic scholars are able to fold those issues within a less rigid conception of God and the world.

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Tussen sciëntisme en fideïsme: Acceptatie van de evolutietheorie als theologische uitdaging

HTS Teologiese Studies / Theological Studies ◽

10.4102/hts.v70i1.2729 ◽

2014 ◽

Vol 70 (1) ◽

Author(s):

Gijsbert Van den Brink

Keyword(s):

Scientific Theory ◽

Natural Theology ◽

Biological Evolution ◽

Evolutionary Development ◽

Special Issue ◽

Theory Of Evolution ◽

Philosophy Of Life ◽

Acceptance Of Evolution ◽

Theological Challenge ◽

Life On Earth

Between scientism and fideism: Acceptance of evolution as a theological challenge. In this contribution to the special issue of HTS Teologiese Studies/Theological Studies that is dedicated to Prof. Buitendag, I will explore what Prof. Buitendag’s notion of a ‘revised natural theology’ might mean for the theological reception of the scientific theory of biological evolution. I argue that two extremes must be avoided here. One is the fideistic ignoring of (or refusal to take into account) the data that have been placed on the table regarding the evolutionary development of life on earth, as if these do not concern theology. The other extreme that theology must steer clear of is a scientistic over-interpretation of our knowledge of the evolutionary past, whereby the theory of evolution is magnified to a comprehensive philosophy of life (‘evolutionism’) that is incompatible with Christian faith.

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Associations between depth and micro-diversity within marine viral communities revealed through metagenomics

10.1101/551291 ◽

2019 ◽

Author(s):

FH Coutinho ◽

R Rosselli ◽

F Rodríguez-Valera

Keyword(s):

Marine Ecosystems ◽

Replication Proteins ◽

Synonymous Mutations ◽

Genes Encoding ◽

Marine Viruses ◽

Viral Communities ◽

Depth Gradients ◽

Seawater Samples ◽

Biological Entities ◽

Bathypelagic Zone

AbstractViruses are extremely abundant and diverse biological entities that contribute to the functioning of marine ecosystems. Despite their recognized importance no studies have addressed trends of micro-diversity in marine viral communities across depth gradients. To fill this gap we obtained metagenomes from both the cellular and viral fractions of Mediterranean seawater samples spanning the epipelagic to the bathypelagic zone at 15, 45, 60 and 2000 meters deep. The majority of viral genomic sequences obtained were derived from bacteriophages of the order Caudovirales, and putative host assignments suggested that they infect some of the most abundant bacteria in marine ecosystems such as Pelagibacter, Puniceispirillum and Prochlorococcus. We evaluated micro-diversity patterns by measuring the accumulation of synonymous and non-synonymous mutations in viral genes. Our results demonstrated that the degree of micro-diversity differs among genes encoding metabolic, structural, and replication proteins and that the degree of micro-diversity increased with depth. These trends of micro-diversity were linked to the changes in environmental conditions observed throughout the depth gradient, such as energy availability, host densities and proportion of actively replicating viruses. These observations allowed us to generate hypotheses regarding the selective pressures acting upon marine viruses from the epipelagic to the bathypelagic zones.

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Exploring the phylogeny of rosids with a five-locus supermatrix from GenBank

10.1101/694950 ◽

2019 ◽

Cited By ~ 1

Author(s):

Miao Sun ◽

Ryan A. Folk ◽

Matthew A. Gitzendanner ◽

Stephen A. Smith ◽

Charlotte Germain-Aubrey ◽

...

Keyword(s):

Sequence Data ◽

Tree Of Life ◽

Divergence Times ◽

Sequencing Technology ◽

Data Set ◽

Important Resource ◽

Current Sampling ◽

Angiosperm Species

AbstractCurrent advances in sequencing technology have greatly increased the availability of sequence data from public genetic databases. With data from GenBank, we assemble and phylogenetically investigate a 19,740-taxon, five-locus supermatrix (i.e., atpB, rbcL, matK, matR, and ITS) for rosids, a large clade containing over 90,000 species, or approximately a quarter of all angiosperms (assuming an estimate of 400,000 angiosperm species). The topology and divergence times of the five-locus tree generally agree with previous estimates of rosid phylogeny, and we recover greater resolution and support in several areas along the rosid backbone, but with a few significant differences (e.g., the placement of the COM clade, as well as Myrtales, Vitales, and Zygophyllales). Our five-locus phylogeny is the most comprehensive DNA data set yet compiled for the rosid clade. Yet, even with 19,740 species, current sampling represents only 16-22% of all rosids, and we also find evidence of strong phylogenetic bias in the accumulation of GenBank data, highlighting continued challenges for species coverage. These limitations also exist in other major angiosperm clades (e.g., asterids, monocots) as well as other large, understudied branches of the Tree of Life, highlighting the need for broader molecular sampling. Nevertheless, the phylogeny presented here improves upon sampling by more than two-fold and will be an important resource for macroevolutionary studies of this pivotal clade.

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Assembling an illustrated family-level tree of life for exploration in mobile devices

10.1101/2021.08.04.454988 ◽

2021 ◽

Author(s):

Andres A. Del Risco ◽

Diego A. Chacon ◽

Lucia Angel ◽

David A. Garcia

Keyword(s):

Dna Sequences ◽

Morphological Diversity ◽

Mobile App ◽

Tree Of Life ◽

Phylogenetic Studies ◽

Large Trees ◽

Family Level ◽

Phylogenetic Hypotheses ◽

Life On Earth ◽

Diversity Of Life

Since the concept of the tree of life was introduced by Darwin about a century and a half ago, a considerable fraction of the scientific community has focused its efforts on its reconstruction, with remarkable progress during the last two decades with the advent of DNA sequences. However, the assemblage of a comprehensive tree of life for its exploration has been a difficult task to achieve due to two main obstacles: i) information is scattered into a plethora of individual sources and ii) practical visualization tools for exceptionally large trees are lacking. To overcome both challenges, we aimed to synthetize a family-level tree of life by compiling over 1400 published phylogenetic studies, ensuring that the source trees represent the best phylogenetic hypotheses to date based on a set of objective criteria. Moreover, we dated the synthetic tree by employing over 550 secondary-calibration points, using publicly available sequences for more than 5000 taxa, and by incorporating age ranges from the fossil record for over 2800 taxa. Additionally, we developed a mobile app (Tree of Life) for smartphones in order to facilitate the visualization and interactive exploration of the resulting tree. Interactive features include an easy exploration by zooming and panning gestures of touch screens, collapsing branches, visualizing specific clades as subtrees, a search engine, a timescale to determine extinction and divergence dates, and quick links to Wikipedia. Small illustrations of organisms are displayed at the tips of the branches, to better visualize the morphological diversity of life on earth. Our assembled Tree of Life currently includes over 7000 taxonomic families (about half of the total family-level diversity) and its content will be gradually expanded through regular updates to cover all life on earth at family-level.

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Biological evolution

10.1093/oso/9780198808282.003.0012 ◽

2018 ◽

Author(s):

Andrew Briggs ◽

Hans Halvorson ◽

Andrew Steane

Keyword(s):

Design Education ◽

Evolutionary Biology ◽

Evolutionary History ◽

Biological Evolution ◽

Sequence Of Events ◽

Living Things ◽

History Of ◽

Informed Opinion ◽

Life On Earth ◽

Insight Into

The chapter discusses the history of life on Earth, and the lessons to be learned from the neo-Darwinian synthesis of evolutionary biology. The long and complex sequence of events in the evolutionary history of life on Earth requires considered interpretation. The neo-Darwinian synthesis is well-supported by evidence and gives rich insight into this process, but does not itself furnish a complete explanation or understanding of living things. This is because a process of exploration can only explore; it cannot fully dictate and can only partially constrain what type of thing will be found. What is found is constrained by other considerations, such as what is possible, and what can make sense. A brief critique of some of Richard Dawkins’ work is given, and also of the movement known as ‘Intelligent Design’. Education policy is well served by a fair appraisal of informed opinion in this area.

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The Quickening of Chemistry

The Fractal Self ◽

10.21313/hawaii/9780824866617.003.0003 ◽

2017 ◽

Author(s):

John L. Culliney ◽

David Jones

Keyword(s):

Living Cells ◽

Molecular Structures ◽

Complex Molecules ◽

Competition And Cooperation ◽

Creation Science ◽

Dna And Rna ◽

Evolution Of Life ◽

Biochemical Research ◽

Life On Earth ◽

The Universe

For billions of years, competition and cooperation (or attractive forces) oscillated in influence in the evolution of the universe. Consistently, the latter prevailed with a slight edge in that affinitive entities in the universe were free to associate, bond, assemble, facilitate, and cooperate, rise above the leveling action of competition, and generate emergence on progressively higher levels: chemical, biological, and social. This chapter returns to cooperation and examines its constructive power in what might be termed ascendant chemistry—the self-organization of molecules and catalysis that led through pathways of burgeoning complexity to the threshold of biology and the evolution of life on earth. Against the illogic of “creation science,” modern biochemical research illuminates how life arose as an assemblage of complex molecules with strong cooperative tendencies within and among themselves. Carbon’s capacity to build with itself and other elements tremendously variable molecular structures with interlocking functions—most notably of the four basic complex chemicals of life: proteins, carbohydrates, lipids, and nucleic acids (DNA and RNA)—ultimately led to the evolution of living cells.

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