The Tree of Life

8 Key excerpts on "The Tree of Life"

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  Astrobiology

  Understanding Life in the Universe

  • Charles S. Cockell(Author)
  • 2020(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  taxon (plural taxa). This hierarchical classification of species has stood the test of time and is today the basis of our way of classifying species.

  8.4 The Tree of Life and Some Definitions

  A tree of life is a diagram used to depict the evolutionary relationships between organisms. Some trees of life depict all three domains of life (Figure 8.3 ), but a phylogenetic tree can in principle contain any organisms of interest, from just a few species to many species across all three domains.

  Figure 8.3 shows a basic phylogenetic tree with some putative relationships between the three domains. Each line denotes an evolutionary “distance” between the groups shown, which reflects the time since they split from a common ancestor. There is no special significance to the groups shown. They merely illustrate some examples. You will notice that the tree is “rooted” in a single ancestor. This is generally called the Last Universal Common Ancestor or LUCA.

  What do phylogenetic trees show us? Phylogenetic trees show patterns of descent. In Figure 8.3 a you can see an example of another phylogenetic tree of large mammals. Let's examine this tree a little more. You'll notice that unlike the tree in Figure 8.3 , it is laid out with horizontal and vertical lines. This immediately shows us that phylogenetic relationships can be represented in different ways. The format shown in Figure 8.4 is typical. In this format, the horizontal lines or “branches” might correspond to the time since two groups or species diverged, or they could correspond to the amount of genetic change between different groups or species. The vertical lines in the tree represent branching into two new groups or species. The vertical line depicts a split at a node, which defines the point (the time) at which a cohesive population divided into two genetically distinct populations. These separations are caused by different effects. For example, two populations of the same organism might be isolated by a mountain range. Over time they diverge and become two different species in response to their different environments. A new forest might separate two groups of the same species inhabiting grassland, and they might evolve separately. The geographical separation of two populations that then evolve independently is called allopatric speciation. Alternatively, two populations might take up two different life styles in the same geographical location, which eventually leads to them becoming distinct species by evolution. This is called sympatric speciation

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  Understanding Metaphors in the Life Sciences

  • Andrew S. Reynolds(Author)
  • 2022(Publication Date)
  • Cambridge University Press

    (Publisher)

  The Tree of Life was a particularly apt metaphor to capture the current rela- tionship among extant species (using the analogy of a genealogical or family tree of relations), but it also vividly captured the dynamic and historical Figure 6.1 Charles Darwin’s “Tree of Life” notebook sketch (public domain). EVOLUTION 101 development of those relationships via the image of the growth of a tree with many branches, some of them dying and producing no further growth, while others remain vibrant and continue to bud off new shoots which will eventu- ally become branches in their own right. Reflecting on the implications of the tree metaphor, Darwin said, “The terms used by naturalists of affinity, relation- ship, community of type, paternity, morphology, adaptive characters, rudi- mentary and aborted organs, &c., will cease to be metaphorical, and will have a plain signification.” Darwin’s tree diagram inspired the German zoologist Haeckel to draw his own series of phylogenetic trees depicting the evolutionary histories of various groups of animals and of life in general. But where Darwin’s image employed a minimalistic line sketch with a tree-like structure, Haeckel, who was a gifted artist, used tall and sturdy oak-like trees as his model (Figure 6.3). Figure 6.2 Tree of Life (Darwin, C. (1859). On the Origin of Species by Means of Natural Selection or The Preservation of Favoured Races in the Struggle for Life. First edition. London: John Murray (public domain)). 102 UNDERSTANDING METAPHORS IN THE LIFE SCIENCES Figure 6.3 The stem tree of man (Haeckel, E. (1897). The Evolution of Man: A Popular Exposition of the Principal Points of Human Ontogeny and Phylogeny. New York: Appleton & Co., plate xv. (public domain)). EVOLUTION 103 Note that despite the accurate realism of Haeckel’s trees, several con- ventions used in their construction are discernible.

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  Eden's Endemics

  Narratives of Biodiversity on Earth and Beyond

  • Elizabeth Callaway(Author)
  • 2020(Publication Date)
  • University of Virginia Press

    (Publisher)

  23 In modern supertrees, the center of the grandest phylogeny is literally the origin of life itself. The complete evolutionary tree is a new creation story, describing visually how all biota grew from a singular origin in time and space. If this is a tree whose beginnings were at the beginning of life, then the events that can be marked along its rings are not just the whole of human history but the entirety of life history. It is the story of the dawn of life, the creation of species through time, and the naming of all those (discovered) species that now cling, dive, or burrow into the surface of the globe, just as they cling to the circumference of the phylogeny in a fine downy fuzz.

  The weight given to the origin of life in these phylogenies underscores the supertrees’ imaginative resonances with Eden. If chapter 1’s GENESYS database implies the future story of a new Eden, one that comes after a plant apocalypse, then supertrees are a new version of the original Genesis, the story of how all we see came to be. Many contemporary phylogenies openly draw on religious associations with The Tree of Life by explicitly naming themselves after it. There is the “Interactive Tree of Life,”24 the “Open Tree of Life,”25 and the “Tree of Life Web Project,”26 among others. Ostensibly these phylogenies are named “trees of life” because they are branching hierarchical networks that include all life, but this naming convention hints at an alignment with religious Trees of Life and also manifests itself in attitudes toward species death and immortality.

  The fact that these trees literally center on the inception of all life makes them into a new genre of origin story, one that, like Genesis, is involved in the naming of all species and characterized by mythic, golden-age abundance. These trees are not the origin story of the creation of the universe, however, but the origin story of biological diversity. They show the exponential creation of diversity through time from the beginning of life (or the beginning of mammals or birds or whatever group of organisms is featured in a tree) up to the rich abundance encountered today. They trace the forking path that led to today’s particular arrangement of biodiversity. But this recognition of phylogenetic trees as the origin stories for biodiversity also points to the potential difficulty of using them in a time in which more diversity is being lost than created.

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  Concepts of Biology

  • Samantha Fowler, Rebecca Roush, James Wise(Authors)
  • 2016(Publication Date)
  • Openstax

    (Publisher)

  (credit: modification of work by Eric Gaba) The phylogenetic tree in Figure 12.2 illustrates the pathway of evolutionary history. The pathway can be traced from the origin of life to any individual species by navigating through the evolutionary branches between the two points. Also, by starting with a single species and tracing backward to any branch point, the organisms related to it by various degrees of closeness can be identified. A phylogeny is the evolutionary history and the relationships among a species or group of species. The study of organisms with the purpose of deriving their relationships is called systematics. Many disciplines within the study of biology contribute to understanding how past and present life evolved over time, and together they contribute to building, updating, and maintaining the “tree of life.” Information gathered may include data collected from fossils, from studying morphology, from the structure of body parts, or from molecular structure, such as the sequence of amino acids in proteins or DNA nucleotides. By considering the trees generated by different sets of data scientists can put together the phylogeny of a species. Scientists continue to discover new species of life on Earth as well as new character information, thus trees change as new data arrive. The Levels of Classification Taxonomy (which literally means “arrangement law”) is the science of naming and grouping species to construct an internationally shared classification system. The taxonomic classification system (also called the Linnaean system after its inventor, Carl Linnaeus, a Swedish naturalist) uses a hierarchical model. A hierarchical system has levels and each group at one of the levels includes groups at the next lowest level, so that at the lowest level each member belongs to a series of nested groups. An analogy is the nested series of directories on the main disk drive of a computer.

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  Biology 2e

  • Mary Ann Clark, Jung Choi, Matthew Douglas(Authors)
  • 2018(Publication Date)
  • Openstax

    (Publisher)

  20 | PHYLOGENIES AND THE HISTORY OF LIFE Figure 20.1 A bee's life is very different from a flower's, but the two organisms are related. Both are members of the domain Eukarya and have cells containing many similar organelles, genes, and proteins. (credit: modification of work by John Beetham) Chapter Outline 20.1: Organizing Life on Earth 20.2: Determining Evolutionary Relationships 20.3: Perspectives on the Phylogenetic Tree Introduction This bee and Echinacea flower (Figure 20.1) could not look more different, yet they are related, as are all living organisms on Earth. By following pathways of similarities and changes—both visible and genetic—scientists seek to map the evolutionary past of how life developed from single-celled organisms to the tremendous collection of creatures that have germinated, crawled, floated, swum, flown, and walked on this planet. 20.1 | Organizing Life on Earth By the end of this section, you will be able to do the following: • Discuss the need for a comprehensive classification system • List the different levels of the taxonomic classification system • Describe how systematics and taxonomy relate to phylogeny • Discuss a phylogenetic tree's components and purpose In scientific terms, phylogeny is the evolutionary history and relationship of an organism or group of organisms. A phylogeny describes the organisim's relationships, such as from which organisms it may have evolved, or to Chapter 20 | Phylogenies and the History of Life 537 which species it is most closely related. Phylogenetic relationships provide information on shared ancestry but not necessarily on how organisms are similar or different. Phylogenetic Trees Scientists use a tool called a phylogenetic tree to show the evolutionary pathways and connections among organisms. A phylogenetic tree is a diagram used to reflect evolutionary relationships among organisms or groups of organisms.

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  Welcome to the Genome

  A User's Guide to the Genetic Past, Present, and Future

  • Robert DeSalle, Michael Yudell(Authors)
  • 2020(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  Although natural selection favors organisms and populations of organisms that are best suited for a particular environment, it is important to realize that the environment can change, suddenly rewriting the selection criteria. An asteroid can hit the Earth or an ice age can cover the planet. In either case, the rules of the game are now different: Species or individuals within a species best suited to survive in the new environment will thrive, and those formerly best suited to the environment will lose their advantage. Because this type of change takes place over such a protracted period—often millions of years—there is something almost unbelievable about evolution. The evolutionary clock ticks at a pace almost impossible for humans to comprehend. But when you begin to look at the ways in which many species resemble one another, at the evidence found in the fossil record, and at DNA extracted from both fossilized and living organisms and see genetic similarity across a wide range of species, the biological reality of evolution becomes obvious.

  The ability to compare and contrast genomes is an essential component of genomics. Thanks to new concepts and technical applications, this process is becoming faster and easier. One of the most important tools is what is known as the “tree of life”—a genealogy of life on Earth, both living and extinct. The tree, with a trunk representing ancestral characteristics, branches off into the different kingdoms of life and fills its branches with Earth’s rich diversity of plants, animals, and microorganisms. Looking at the tree you can see the evolutionary relationships among all living species and their extinct ancestors. (21 )

  The idea of organizing life on Earth by relatedness has a rich tradition. In the eighteenth century, the Swedish botanist Linnaeus organized all living species into a nonevolutionary semi‐hierarchical taxonomic scheme he called the Systema naturae. Life was organized into kingdoms, phyla, classes, orders, families, genera, and species. (22 ) In the Origin of Species Darwin integrated the Systema naturae with his theory of evolution in a tree of life that linked the evolutionary relationships of different species. (23

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  Demons in Eden

  The Paradox of Plant Diversity

  • Jonathan Silvertown(Author)
  • 2008(Publication Date)
  • University of Chicago Press

    (Publisher)

   The Tree of Trees Throughout the fourteen chapters of The Origin of Species, there is but one illustration. It is a tree: an evolutionary tree. No other metaphor so compactly and completely sums up what evolution is all about. Tracing branches downward from branch tips to root emphasizes the common ancestry of all life. Following the tree upward from root to branches emphasizes the evolution of diversity, but not all branches lead to the crown of the tree. Some whole limbs have snapped o ff : they have no living descendants. Others have branched profusely and tens of thousands of living species blossom in the canopy. Darwin be-lieved that representing the relationship among groups of living things in the form of a tree was no mere metaphor, that it “largely speaks the truth”: As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by gener-ation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications. If Darwin were writing today, a tree would undoubtedly be his logo. The dead and broken branches that encrust the Earth are species known only as fossils, such as the giant lycopods and seed ferns that grew in the swamps during the carboniferous period and later became coal. Limestones such as chalk are the fossil remains of tiny creatures whose shells accumulated over millions of years in ma-rine sediments. It is estimated that at least  percent of all species that have ever lived are now extinct. The species alive today are the outermost branch tips of a very an-cient tree. If we want to understand the history of evolution and where present-day biodiversity comes from, we must reconstruct The Tree of Life. In this exciting scientific enterprise, botanists have been in the vanguard and zoologists, for once, in the guard’s van. In its es-

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  Life in Space

  Astrobiology for Everyone

  • Lucas John Mix(Author)
  • 2009(Publication Date)
  • Harvard University Press

    (Publisher)

  17 The Tree of Life No discussion of life on Earth would be complete without some attempt to look at the diversity and interrelation of organisms. Chapter 15 intro-duced taxonomy, the classification and naming of organisms. In this chap-ter, I will go into much greater detail, looking at the history of the field as well as the state of the art. We will look at several historical systems before diving into the most popular system today: molecular phylogenetics. We will explore the three domains—Archaea, Bacteria, and Eukarya—that constitute the terrean biosphere. The next chapter addresses a few excep-tional entities that blur the lines between life and nonlife and, therefore, do not fall under the current classification scheme. Of course, names say something significant about the namer. They come deeply embedded in how we see the world and what we look for. Astrobiologists are keenly aware of how various forms of life are classified because often such classifi-cations inform them about the origins, extent, and definition of life. Biology textbooks often begin with taxonomy. Establishing a structure first allows discussions of evolution, structure, and biochemistry to occur in the context of many specific examples. Biologists tend to catalog diver-sity, dropping individual creatures in a series of bins, whereas astrobiolo-gists are more concerned with the context in which life occurs. I have put off this chapter as long as possible in the hopes of presenting a picture of life as a planetary phenomenon. All terrean life operates in the same way, 246 LIFE IN SPACE with the same bottom-up structure, using the same molecules and metab-olism, and always interacting as a unit, a biosphere. Rare metabolisms, like hydrogen gas chemotrophy, exist only in the context of a larger commu-nity. Hydrogen gas usually happens only around other organisms. Like-wise, the deep-sea vent communities depend upon fixed carbon sinking from the surface of the ocean.

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