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6.8: Introduction to Phylogenies and the History of Life - Biology

6.8: Introduction to Phylogenies and the History of Life - Biology



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Read and analyze a phylogenetic tree that documents evolutionary relationships

This bee and Echinacea flower (Figure 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, swam, flown, and walked on this planet.

What You’ll Learn to Do

  • Discuss the components and purpose of a phylogenetic tree
  • List the different levels of the taxonomic classification system
  • Compare homologous and analogous traits
  • Discuss the purpose of cladistics
  • Identify different perspectives and criticisms of the phylogenetic tree

Learning Activities

The learning activities for this section include the following:

  • Phylogenetic Trees
  • Taxonomy
  • Homologous and Analogous Traits
  • Cladistics
  • Perspectives on the Phylogenetic Tree
  • Self Check: Phylogenies and the History of Life

Figure 6.8 Look at each of the processes shown, and decide if it is endergonic or exergonic. In each case, does enthalpy increase or decrease, and does entropy increase or decrease?

Figure 6.8 Look at each of the processes shown, and decide if it is endergonic or exergonic. In each case, does enthalpy increase or decrease, and does entropy increase or decrease?

To discuss exergonic or endergonic reaction in given conditions.

Introduction:

Synthesis of complex molecules from simpler ones by using energy is called the anabolic process. It is an endergonic process. In contrast, the breakdown of complex molecules into simpler ones is the catabolic process. Energy is released in this process, it is an exergonic process.

Explanation of Solution

The processes given in the figure can be classified as exergonic or endergonic as follows:

  1. A compost pile decomposing is an exergonic process as energy is being released. Enthalpy increases due to energy release and entropy also increase as large molecules broken into smaller ones.
  2. A chick developing from a fertilized egg requires energy, so this is an endergonic reaction. Due to the absorption of energy enthalpy decreases. Entropy decreases as large molecules are formed from the small molecules.
  3. Sand art is being destroyed which is an exergonic reaction. Enthalpy remains same as there is no change in the total energy, but entropy increases as smaller molecules combine to form large molecules.
  4. A ball rolling down the hill is an exergonic reaction as it releases energy and enthalpy decreases. But there is no change in entropy.

An endergonic reaction is that reaction which requires energy and exergonic reaction are those reactions which release energy. Enthalpy is the total energy of the system whereas entropy measures the disorder within the system.

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Visual Connection Questions

Figure 6.8 Look at each of the processes, and decide if it is endergonic or exergonic. In each case, does enthalpy increase or decrease, and does entropy increase or decrease?

Figure 6.10 If no activation energy were required to break down sucrose (table sugar), would you be able to store it in a sugar bowl?

Figure 6.14 One ATP molecule's hydrolysis releases 7.3 kcal/mol of energy (∆G = −7.3 kcal/mol of energy). If it takes 2.1 kcal/mol of energy to move one Na + across the membrane (∆G = +2.1 kcal/mol of energy), how many sodium ions could one ATP molecule's hydrolysis move?

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    61 Introduction

    The leaf chameleon (Brookesia micra) was discovered in northern Madagascar in 2012. At just over one inch long, it is the smallest known chameleon. (credit: modification of work by Frank Glaw, et al., PLOS)

    While we can easily identify dogs, lizards, fish, spiders, and worms as animals, other animals, such as corals and sponges, might be easily mistaken as plants or some other form of life. Yet scientists have recognized a set of common characteristics shared by all animals, including sponges, jellyfish, sea urchins, and humans.

    The kingdom Animalia is a group of multicellular Eukarya. Animal evolution began in the ocean over 600 million years ago, with tiny creatures that probably do not resemble any living organism today. Since then, animals have evolved into a highly diverse kingdom. Although over one million currently living species of animals have been identified, scientists are continually discovering more species. The number of described living animal species is estimated to be about 1.4 million, 1 and there may be as many as 6.8 million.

    Understanding and classifying the variety of living species helps us to better understand how to conserve and benefit from this diversity. The animal classification system characterizes animals based on their anatomy, features of embryological development, and genetic makeup. Scientists are faced with the task of classifying animals within a system of taxonomy that reflects their evolutionary history. Additionally, they must identify traits that are common to all animals as well as traits that can be used to distinguish among related groups of animals. However, animals vary in the complexity of their organization and exhibit a huge diversity of body forms, so the classification scheme is constantly changing as new information about species is learned.


    INTRODUCTION TO PHYLOGENETICS.

    From the time of Charles Darwin, it has been the dream of many biologists to reconstruct the evolutionary history of all organisms on Earth and express it in the form of a phylogenetic tree. Phylogeny uses evolutionary distance, or evolutionary relationship, as a way of classifying organisms (taxonomy).

    Phylogenetic relationship between organisms is given by the degree and kind of evolutionary distance. To understand this concept better, let us define taxonomy. Taxonomy is the science of naming, classifying and describing organisms. Taxonomists arrange the different organisms in taxa (groups). These are then further grouped together depending on biological similarities. This grouping of taxa reflects the degree of biological similarity.

    Systematics takes taxonomy one step further by elucidating new methods and theories that can be used to classify species. This classification is based on similarity traits and possible mechanisms of evolution. In the 1950s, William Hennig, a German biologist, proposed that systematics should reflect the known evolutionary history of lineages, an approach he called phylogenetic systematics. Therefore, phylogenetic systematics is the field that deals with identifying and understanding the evolutionary relationships among many different kinds of organisms

    Phylogenic relationships have been traditionally studied based on morphological data. Scientists used to examine different traits or characteristics and tried to establish the degree of relatedness between organisms. Then scientists realized that not all shared characteristics are useful in studying relationships between organisms. This discovery led to a study of systematics called cladistics. Cladistics is the study of phylogenetic relationships based on shared, derived characteristics. There are two types of characteristics, primitive traits and derived traits, which are described below.

    Primitive traits are characteristics of organisms that were present in the ancestor of the group that is under study. They do not indicate anything about the relationships of species within a group because they are inherited from the ancestor to all of the members of the group. Derived traits are characteristics of organisms that have evolved within the group under study. These characteristics were not present in the ancestor. They are useful because they can help explain why some species have common traits. The most likely explanation for the presence of a trait that was not present in the ancestor of the whole group is that it evolved from a more recent ancestor.

    Two extensive groups of analyses exist to examine phylogenetic relationships: Phenetic methods and cladistic methods. Phenetic methods, or numerical taxonomy, use various measures of overall similarity for the ranking of species. They can use any number or type of characters, but the data has to be converted into a numerical value. The organisms are compared to each other for all of the characters and then the similarities are calculated. After this, the organisms are clustered based on the similarities. These clusters are called phenograms. They do not necessarily reflect evolutionary relatedness. The cladistic method is based on the idea that members of a group share a common evolutionary history and are more closely related to members of the same group than to any other organisms. The shared derived characteristics are called synapomorphies.

    The introduction of two important tools has dramatically improved the study of phylogenetics. The first tool is the development of computer algorithms capable of constructing phylogenetic trees. The second tool is the use of molecular sequence data for phylogenetic studies.

    Phylogenetics can use both molecular and morphological data in order to classify organisms. Molecular methods are based on studies of gene sequences. The assumption of this methodology is that the similarities between genomes of organisms will help to develop an understanding of the taxonomic relationship among these species. Morphological methods use the phenotype as the base of phylogeny. These two methods are related since the genome strongly contributes to the phenotype of the organisms. In general, organisms with more similar genes are more closely related. The advantage of molecular methods is that it makes possible the study of genes without a morphological expression.

    As previously mentioned, closely related species share a more recent common ancestor than distantly related species. The relationships between species can be represented by a phylogenetic tree. This is a graphical representation that has nodes and branches. The nodes represent taxonomic units. Branches reflect the relationships of these nodes in terms of descendants. The branch length usually indicates some form of evolutionary distance. The actual existing species called the operational taxonomic units (OTUs) are at the tip of the branches on the external nodes.

    Tree construction methods
    Some methods have been proposed for the construction of phylogenetic trees. They can be classified into two groups, the cladistic methods (maximum parsimony and maximum likelihood) and the phenetic method (distance matrix method).

    Maximum parsimony trees imply that simple hypotheses are more preferable than complicated ones. This means that the construction of the tree using this method requires the smallest number of evolutionary changes in order to explain the phylogeny of the species under study. In the procedure, this method compares different parsimonious trees and chooses the tree that has the least number of evolutionary steps (substitutions of nucleotides in the context of DNA sequence).

    Maximum likelihood This method evaluates the topologies of different trees and chooses the best based on a specified model. This model is based on the evolutionary process that can account for the conversion of one sequence into another. The parameter considered in the topology is the branch length.

    Distance matrix is a phenetic approach preferred by many molecular biologists for DNA and protein work. This method estimates the mean number of changes (per site in sequence) in two taxa that have descended from a common ancestor. There is much information in the gene sequences that must be simplified in order to compare only two species at a time. The relevant measure is the number of differences in these two sequences, a measure that can be interpreted as the distance between the species in terms of relatedness.

    Molecular phylogeny was first suggested in 1962 by Pauling and Zuckerkandl. They noted that the rates of amino acid substitution in animal hemoglobin were roughly constant over time. They described the molecules as documents of evolutionary history. The molecular method has many advantages. Genotypes can be read directly, organisms can be compared even if they are morphologically very different and this method does not depend on phenotype.

    Phylogeny is currently used in many fields such as molecular biology, genetics, evolution, development, behaviour, epidemiology, ecology, systematics, conservation biology, and forensics. Biologists can infer hypotheses from the structure of phylogenetic trees and establish models of different events in evolutionary history. Phylogeny is an exceptional way to organize evolutionary information. Through these methods, scientists can analyse and elucidate different processes of life on Earth.

    Today, biologists calculate that there are about 5 to 10 million species of organisms. Different lines of evidence, including gene sequencing, suggest that all organisms are genetically related and may descend from a common ancestor. This relationship can be represented by an evolutionary tree, like the Tree of Life. The Tree of Life is a project that is focused on understanding the origin of diversity among species using phylogeny.

    References:
    1) Whelan S., Lio P., Goldman N., (2001)Molecular phylogenetics: state-of-the-art methods for looking into the past Trends in Genetics, Volume 17, Issue 5, 1, Pages 262-272

    2) Berger J. Introduction to Molecular Phylogeny Construction. BIOL 334.

    3) Wen-Hsiung Li. Molecular Evolution. Sinauer Associates, 1997.

    4) Pagel, M. (1999) Inferring historical patterns of biological evolution. Nature 401, 877–884

    5) Zuckerlandl, E. and Pauling, L. (1962) Molecular disease, evolution, and genetic heterogeneity. In Horizons in Biochemistry (Kasha,M. and Pullman, B., eds), pp. 189–225, Academic Press 1921–1930

    6) Felsenstein, J. (1981), Evolutionary trees from DNA sequences: a maximum likelihood approach, Journal of Molecular Evolution 17:368-376

    7) Endo T., Ogishima S., Tanaka H. (2003) Standardized phylogenetic tree: a reference to discover functional evolution J Mol Evol 57 Suppl 1:S174-81. Plant Species Biology

    8) Murren C. (2002) Phenotypic integration in plants. Plant Species Biology. Volume 17 Issue 2-3 Page 89


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    Campbell Biology / Lisa A. Urry, Mills College, Oakland, California, Michael L. Cain, Bowdoin College, Brunswick, Maine, Steven A. Wasserman, University of California, San Diego, Peter V. Minorsky, Mercy College, Dobbs Ferry, New York, Jane B. Reece, Berkeley, California.

    This edition was published in 2017 by Pearson Education, Inc. in New York, NY .

    Edition Description

    1 volume (various pagings) : illustrations (chiefly color), color maps 29 cm


    Phylogenetic Analysis: Early Evolution of Life

    Tracing the Evolutionary Steps Using Phylogeny

    Phylogeny can be described as the relationship between all the organisms on Earth that have descended from a common ancestor, whether they are extinct or extant. Phylogenetics is the science of studying the evolutionary relatedness among biological groups and a phylogenetic tree is used to graphically represent this evolutionary relation related to the species of interest ( Figs. 9–11 ).

    Fig. 9 . Phylogenetic tree of contemporary organisms.

    Fig. 10 . Phylogenetic tree of bacteria.

    Fig. 11 . Elements of a typical phylogram.

    More specialized phylogenetic methods have been developed now to meet specific needs, such as species and molecular phylogenetic tests, biogeographic hypotheses, testing, for evaluating amino acids of extinct or extant proteins, establish disease epidemiology and evolution, and even in forensic studies ( Linder and Warnow, 2005 ).


    Play Build A Tree

    Start by building your own phylogenetic trees by analyzing the traits and DNA that characterize selected species. We’ve produced a series of puzzles, animated videos, and background information to lead you through levels that start out simple and build in complexity:

    • Training Trees is an introduction to the structure of phylogenetic trees and explains how to build and read them
    • Fossils: Rocking the Earth explains how fossils help us understand the history of life on Earth
    • DNA Spells Evolution explains how DNA provides a genetic record of changes that have occurred in a species over time and insights into the relationships among organisms
    • Biogeography: Where Life Lives explains how phylogenetic trees can help us understand the movement of organisms across space and time
    • Tree of Life and Death introduces several applications of phylogenetic trees for understanding and treating diseases and
    • You Evolved Too examines the relatively recent appearance of human beings in the tree of life.

    The History of Life on Earth

    Life on Earth has been changing at various rates since our common ancestor first appeared more than 3.5 billion years ago. To better understand the changes that have taken place, it helps to look for milestones in the history of life on Earth. By grasping how organisms, past and present, have evolved and diversified throughout the history of our planet, we can better appreciate the animals and wildlife that surround us today.

    The first life evolved more than 3.5 billion years ago. Scientists estimate that the Earth is some 4.5 billion years old. For nearly the first billion years after the Earth formed, the planet was inhospitable to life. But by about 3.8 billion years ago, the Earth's crust had cooled and the oceans had formed and conditions were more suitable for the formation of life. The first living organism formed from simple molecules present in the Earth's vast oceans between 3.8 and 3.5 billion years ago. This primitive life form is know as the common ancestor. The common ancestor is the organism from which all life on Earth, living and extinct, descended.

    Photosynthesis arose and oxygen began accumulating in the atmosphere about 3 billion years ago. A type of organism known as cyanobacteria evolved some 3 billion years ago. Cyanobacteria are capable of photosynthesis, a process by which energy from the sun is used to convert carbon dioxide into organic compounds—they could make their own food. A byproduct of photosynthesis is oxygen and as cyanobacteria persisted, oxygen accumulated in the atmosphere.

    Sexual reproduction evolved about 1.2 billion years ago, initiating a rapid increase in the pace of evolution. Sexual reproduction, or sex, is a method of reproduction that combines and mixes traits from two parent organisms in order to give rise to an offspring organism. Offspring inherit traits from both parents. This means that sex results in the creation of genetic variation and thus offers living things a way to change over time—it provides a means of biological evolution.

    The Cambrian Explosion is the term given to the time period between 570 and 530 million years ago when most modern groups of animals evolved. The Cambrian Explosion refers to an unprecedented and unsurpassed period of evolutionary innovation in the history of our planet. During the Cambrian Explosion, early organisms evolved into many different, more complex forms. During this time period, nearly all of the basic animal body plans that persist today came into being.

    The first back-boned animals, also known as vertebrates, evolved about 525 million years ago during the Cambrian Period. The earliest known vertebrate is thought to be Myllokunmingia, an animal that is thought to have had a skull and a skeleton made of cartilage. Today there are about 57,000 species of vertebrates that account for about 3% of all known species on our planet. The other 97% of species alive today are invertebrates and belong to animal groups such as sponges, cnidarians, flatworms, mollusks, arthropods, insects, segmented worms, and echinoderms as well as many other lesser-known groups of animals.

    The first land vertebrates evolved about 360 million years ago. Prior to about 360 million years ago, the only living things to inhabit terrestrial habitats were plants and invertebrates. Then, a group of fishes know as the lobe-finned fishes evolved the necessary adaptations to make the transition from water to land.

    Between 300 and 150 million years ago, the first land vertebrates gave rise to reptiles which in turn gave rise to birds and mammals. The first land vertebrates were amphibious tetrapods that for some time retained close ties with the aquatic habitats they had emerged from. Over the course of their evolution, early land vertebrates evolved adaptations that enabled them to live on land more freely. One such adaptation was the amniotic egg. Today, animal groups including reptiles, birds and mammals represent the descendants of those early amniotes.

    The genus Homo first appeared about 2.5 million years ago. Humans are relative newcomers to the evolutionary stage. Humans diverged from chimpanzees about 7 million years ago. About 2.5 million years ago, the first member of the genus Homo evolved, Homo habilis. Our species, Homo sapiens evolved about 500,000 years ago.


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