Phylogenetic Tree

11 Key excerpts on "Phylogenetic Tree"

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  Cladistics (Method of Classifying Species of Organisms into Groups)

  • (Author)
  • 2014(Publication Date)
  • University Publications

    (Publisher)

  A Phylogenetic Tree represents a hypothesis of the order in which evolutionary events are assumed to have occurred. Cladistics is the current method of choice to infer Phylogenetic Trees. The most commonly-used methods to infer phylogenies include parsimony, maximum likelihood, and MCMC-based Bayesian inference. Phenetics, popular in the mid-20th century but now largely obsolete, uses distance matrix-based methods to construct trees based on overall similarity, which is often assumed to approximate phylogenetic relationships. All methods depend upon an implicit or explicit mathematical model describing the evolution of characters observed in the species included, and are usually used for molecular phylogeny, wherein the characters are aligned nucleotide or amino acid sequences. ________________________ WORLD TECHNOLOGIES ________________________ Grouping of organisms Phylogenetic groups, or taxa , can be monophyletic, paraphyletic, or polyphyletic. There are some terms that describe the nature of a grouping in such trees. For instance, all birds and reptiles are believed to have descended from a single common ancestor, so this taxonomic grouping (yellow in the diagram below) is called monophyletic. Modern reptile (cyan in the diagram) is a grouping that contains a common ancestor, but does not contain all descendants of that ancestor (birds are excluded). This is an example of a paraphyletic group. A grouping such as warm-blooded animals would include only mammals and birds (red/orange in the diagram) and is called polyphyletic because the members of this grouping do not include the most recent common ancestor. Molecular phylogenetics The evolutionary connections between organisms are represented graphically through Phylogenetic Trees. Due to the fact that evolution takes place over long periods of time

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  Mathematical Concepts and Methods in Modern Biology

  Using Modern Discrete Models

  • Raina Robeva, Terrell Hodge(Authors)
  • 2013(Publication Date)
  • Academic Press

    (Publisher)

  [5] . Of course, genetic isolation alone is insufficient to explain diversity, which further requires the raw material of genetic mutation, inevitably acted upon by natural selection.

  A Phylogenetic Tree (or phylogeny ) is a diagram/graph which represents relations of evolutionary descent of different species, organisms, or genes from a common ancestor. A Phylogenetic Tree is a useful tool to understand and organize information on biological diversity, structuring classifications, and providing insight into events that occurred during evolution. An excellent preliminary guide to the biological perspective, upon which we build a more mathematical approach in this chapter, is [6] ; see http://www.nature.com/scitable/topicpage/reading-a-phylogenetic-tree-the-meaning-of-41956 .

  One may reconstruct a Phylogenetic Tree among distinct groups or species from morphological data obtained by measuring and quantifying the phenotypic properties of representative organisms via, for example, parsimony. However, recent phylogenetic analysis uses nucleotide sequences encoding genes or amino acid sequences encoding proteins as the basis for classification. Therefore in this chapter we focus on Phylogenetic Tree reconstruction methods based on sequenced genes or genomic data sets. Through evolutionary history, a character (e.g., a nucleotide) of the sequence might be changed to another one, deleted or inserted. Thus, before reconstructing a Phylogenetic Tree, we have to align an input sequence data set, e.g., identify sequences of characters (DNA bases, amino acids, etc.) which are thought to be representing the same (“homologous”) regions of genes (from different species or different gene families, etc.) and then line up the sequences so that nucleotides in differing sequences can be compared site-by-site, where one site may vary from another by mutation, i.e., insertions, deletions, or substitutions of characters. Such a line-up of two sequences is an alignment ; if we have multiple sequences then the result is properly called a multiple alignment , although we will often abuse terminology and use “alignment” for both. Aligning multiple sequences is generally known to be an NP-hard problem [7 ,8

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  Handbook of Trait-Based Ecology

  From Theory to R Tools

  • Francesco de Bello, Carlos P. Carmona, André T. C. Dias, Lars Götzenberger, Marco Moretti, Matty P. Berg(Authors)
  • 2021(Publication Date)
  • Cambridge University Press

    (Publisher)

  Then, a second explosion of studies and methods has seen community ecologists using phylogenetic 151 relationships as a substitute, or complement, for traits. If you are unable to follow why anyone would arrive at the conclusion that it might be reasonable to study communities from a phylogenetic perspective rather than using traits, do not worry, and bear with us. We are going to take it step by step from here, but first, as a short precursor, we will learn how we represent and describe phylogenetic information. Note that we are treating here in a single chapter something that is covered by entire books. So if you want to delve deeper into the ideas presented in this chapter, we refer you to some of the essential literature: Harvey and Pagel (1991) provided the first book-length treatment of the comparative method, and it can be regarded as a classic in the field. Garamszegi (2014) edited a book containing chapters written by many prominent scholars in the field, basically bringing the topic of Harvey and Pagel’s book into the twenty-first century. Both Swenson (2014a) and Paradis (2012) cover the technical and statistical application of the matter, in conjunction with the packages picante and ape, respectively. 8.1 What Is a Phylogenetic Tree? A Phylogenetic Tree is a way to visually represent how species are related to each other through their ancestors (Fig. 8.1). We can think of the ancestors as ‘mother’ species, where each mother has two ‘offspring’. The current species are sometimes called tips or leaves of the tree, each of them being connected to their last ancestor (‘mother’ species). In tree terminology, these ancestors are called nodes, because they are represented in the tree as internal points in the branching structure. Furthermore, just as real trees have a root, so do Phylogenetic Trees, usually.

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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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  Bioinformatics for Beginners

  Genes, Genomes, Molecular Evolution, Databases and Analytical Tools

  • Supratim Choudhuri(Author)
  • 2014(Publication Date)
  • Academic Press

    (Publisher)

  phylogenies—that is, the study of the evolutionary relationships of species. Phylogenetic analysis is the means of estimating the evolutionary relationships. In molecular phylogenetic analysis, the sequence of a common gene or protein can be used to assess the evolutionary relationship of species. The evolutionary relationship obtained from phylogenetic analysis is usually depicted as branching, treelike diagram—the Phylogenetic Tree. Historically, the use of Phylogenetic Trees was restricted more or less to the study of evolutionary biology, and to disciplines like systematics and taxonomy. However, with the advent of sequencing and the widespread use of cladistics, the use of Phylogenetic Trees has pervaded many branches of biology and beyond. Construction of phylogenetic/evolutionary trees is now widespread in many areas of study where evolutionary divergence can be studied and demonstrated; be it pathogens, biological macromolecules, or languages. Phylogenetics also provides the basis for comparative genomics, which is a more recent term that came into existence in the age of genomics. Comparative genomics is the study of the interrelationships of genomes of different species. Comparative genomics helps identify regions of similarity and differences among genomes. The comparison can be made at different levels, such as comparison of whole-genome sequences, comparison of genome sequences involving blocks of conserved synteny, comparison of the number of protein-coding genes, comparison of regulatory sequences, or other focused comparisons. An important application of comparative genomics is gene finding

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  Essential Bioinformatics

  • Jin Xiong(Author)
  • 2006(Publication Date)
  • Cambridge University Press

    (Publisher)

  SECTION FOUR Molecular Phylogenetics CHAPTER TEN Phylogenetics Basics Biological sequence analysis is founded on solid evolutionary principles (see Chapter 2 ). Similarities and divergence among related biological sequences revealed by sequence alignment often have to be rationalized and visualized in the context of Phylogenetic Trees. Thus, molecular phylogenetics is a fundamental aspect of bioinfor-matics. In this chapter, we focus on Phylogenetic Tree construction. Before discussing the methods of Phylogenetic Tree construction, some fundamental concepts and back-ground terminology used in molecular phylogenetics need to be described. This is followed by discussion of the initial steps involved in Phylogenetic Tree construction. MOLECULAR EVOLUTION AND MOLECULAR PHYLOGENETICS To begin the phylogenetics discussion, we need to understand the basic question, “What is evolution?” Evolution can be defined in various ways under different con-texts. In the biological context, evolution can be defined as the development of a biological form from other preexisting forms or its origin to the current existing form through natural selections and modifications. The driving force behind evolution is natural selection in which “unfit” forms are eliminated through changes of environ-mental conditions or sexual selection so that only the fittest are selected. The under-lying mechanism of evolution is genetic mutations that occur spontaneously. The mutations on the genetic material provide the biological diversity within a popula-tion; hence, the variability of individuals within the population to survive successfully in a given environment. Genetic diversity thus provides the source of raw material for the natural selection to act on. Phylogenetics is the study of the evolutionary history of living organisms using tree-like diagrams to represent pedigrees of these organisms. The tree branching patterns representing the evolutionary divergence are referred to as phylogeny.

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  Phylogenetics

  Theory and Practice of Phylogenetic Systematics

  • E. O. Wiley, Bruce S. Lieberman(Authors)
  • 2011(Publication Date)
  • Wiley-Blackwell

    (Publisher)

  Phylogenetic Systematics .

  Copyright 1966, 1979 by the Board of Trustees of the University of Illinois. Used with permission of the author and the University of Illinois Press.

  Analysis of this descent is restricted largely to specimens taken from these populations. Our symbolic representations can be quite simple, but they can be accurate relative to our hypotheses of relationship in the sense that if we knew the relationships we would find that the symbolic representations are logically consistent with those relationships. On the empirical level, we expect the tree to be logically consistent with the evidence at hand. It may be accurate without being complicated because the relationship between tokogeny and phylogeny is hierarchical and nontransitive: tokogenetic systems, if we can observe them, could be translated into phylogenetic systems, but the tokogenetic relationships among individual organisms cannot be recovered from a Phylogenetic Tree as we commonly draw them (Coleman and Wiley, 2001). An analogy is a system of highways: we can map the highways by accounting for every piece of gravel used to construct them, but we cannot account for every piece of gravel by consulting a highway map. Nevertheless, the map gets us where we wish to go; it is an accurate enough graphic representation of the macroscopic properties of the highway even though it does not account for its microscopic properties.

  Consider Fig. 4.1 b. It makes the following statements:

  1. X speciates, giving rise to A and Y.

  2. Y is the parent of B and C.

  3. A, B, and C are species or clades of species.

  4. C is more closely related to B than it is to A because both have the parent Y and A does not.

  Phylogeneticists frequently talk about edges (Fig. 4.1

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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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  Semialgebraic Statistics and Latent Tree Models

  • Piotr Zwiernik(Author)
  • 2015(Publication Date)
  • Chapman and Hall/CRC

    (Publisher)

  Chapter 5 Phylogenetic Trees and their models [] In this chapter, we introduce the main object of study of this book, which are trees and their statistical models. In the beginning, the main motivation will be to provide first examples of how various geometric spaces are associ-ated to trees. We discuss the space of tree metrics, the space of phylogenetic oranges, and the latent tree model. Some necessary combinatorics, including tree splits and the Tuffley poset, provides us a language to describe these spaces and their special points. What we will try to indicate in this chapter and prove in the following ones is that these various tree spaces have many features in common and they should be studied together. We start with some standard definitions. 5.1 Trees 5.1.1 Phylogenetic Trees and semi-labeled trees In Section 3.4.1 we introduced some basic graph-theoretic concepts. In this section we extend this material specializing to trees. A tree T = ( V, E ) is a connected undirected graph with no cycles. In particular, for any two u, v ∈ V there is a unique path between them, which we denote by uv . A vertex of T that has only one neighbor is called a leaf . A vertex of T that is not a leaf is called an inner vertex . An edge of T is inner if both of its ends are inner vertices, otherwise it is called terminal . A connected subgraph of T is called a subtree of T . A rooted tree T r is a directed graph whose underlying undirected graph is a tree that has one distinguished vertex r , called the root , and all the edges are directed away from r . For every vertex v of a rooted tree T r such that v ∈ V r , the set pa( v ) of parents of v is a singleton. As an example consider the quartet tree in Figure 5.1 with one of its rooted versions, where the root is given by an inner vertex. 1 2 3 4 1 2 3 4 Figure 5.1: A quartet tree and a rooted quartet tree. 103 104 Phylogenetic TreeS AND THEIR MODELS We often constrain ourselves to binary trees .

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  Classification and Biology

  • R.A. Crowson(Author)
  • 2017(Publication Date)
  • Routledge

    (Publisher)

  In a phylogenetic system, the various categories could be defined in relation to the various degrees of remoteness of this common ancestral species, measured in years or in generations; it is, in fact, the only type of classification which offers the possibility of really objective criteria for supra-specific categories. The successive divisions in the classificatory hierarchy will then correspond to successive forkings in the ‘family tree’, realising the idea embodied in the Darwinian quotation at the head of this chapter. This phylogenetic definition of a natural classification is quite distinct from the Aristotelean and statistical ones; we may well ask, to what extent will a ‘phylogenetic’ classification be natural according to the other two definitions? The strict answer is, of course, that we do not know, having no classifications which we can be sure are perfectly natural according to any of the three definitions. Probably the majority of zoologists and a minority of botanists share the comfortable faith that in practice all three definitions will lead to the same system; the zoological minority, and the much more considerable botanical fraction, who doubt this are themselves divided on the question—if different definitions of a natural classification lead to different results, which of them should we follow? The botanists could justly point out that the zoological majority, while professing to believe that a natural classification is the same as a phylogenetic one, accept without demur in textbooks etc., classifications which are at variance with the family trees depicted in the same works. The most obvious example concerns the classes of the Vertebrata. Thus in Romer [ 160 ], the ‘dendrograms’ in figures 31-32 show the birds sharing a common ancestor with the crocodiles more recently than the latter group do with snakes and lizards, yet in that work Crocodilia are placed together with Squamata in a class Reptilia while birds form a separate class Aves

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  Bioinformatics: A Swiss Perspective

  A Swiss Perspective

  • Ron D Appel, Ernest Feytmans(Authors)
  • 2009(Publication Date)
  • World Scientific

    (Publisher)

  This section discusses these methods. Many different algorithms exist, and explaining them all in detail is beyond the scope of this chapter. However, most of the algorithms can be grouped together into three main categories. For alternative methods, see Semple and Steel. 1 Before we get down to the details of the three categories, we will describe the theoretical framework common to them all. 4.1. The Tree Graph Model — Transmission of Phylogenetic Information As we have seen, a tree graph, as opposed to a reticular (network-like) graph, has certain inherent properties. For instance, there can only be a single path from one node to another. This holds true for all nodes, whether internal or terminal. Furthermore, when time is taken into account in a Phylogenetic Tree, information always flows in the same direc-tion. Branches are unequivocally oriented from the root to the terminal nodes (in Fig. 7, from node “A” along the respective lineages to “C”, “D”, and “E”). In genealogy (the study of family trees), it is possible for two repre-sentatives of two separate lineages to breed and thereby reconnect their lineages. By contrast, in the phylogenetic model, which applies to a higher taxonomic level than the individual, in principle lineages cannot cross each other. Horizontal gene transfer m is sufficiently rare to be Introduction to Phylogenetics and Its Molecular Aspects 305 m Horizontal gene transfer is the exchange of genetic information through means other than simple heredity. This usually involves transposable elements, viruses, or bacteria. The result is a reticulate phylogenetic network that is no longer a tree. insignificant in most cases (notable exceptions include viruses and bacte-ria). Transfer of genetic information is thus practically always “vertical”.

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