Molecular Evolution (Bioinformatics IV)

Start Date: 07/05/2020

Course Type: Common Course

Course Link: https://www.coursera.org/learn/molecular-evolution

About Course

In the previous course in the Specialization, we learned how to compare genes, proteins, and genomes. One way we can use these methods is in order to construct a "Tree of Life" showing how a large collection of related organisms have evolved over time. In the first half of the course, we will discuss approaches for evolutionary tree construction that have been the subject of some of the most cited scientific papers of all time, and show how they can resolve quandaries from finding the origin of a deadly virus to locating the birthplace of modern humans. In the second half of the course, we will shift gears and examine the old claim that birds evolved from dinosaurs. How can we prove this? In particular, we will examine a result that claimed that peptides harvested from a T. rex fossil closely matched peptides found in chickens. In particular, we will use methods from computational proteomics to ask how we could assess whether this result is valid or due to some form of contamination. Finally, you will learn how to apply popular bioinformatics software tools to reconstruct an evolutionary tree of ebolaviruses and identify the source of the recent Ebola epidemic that caused global headlines.

Course Syllabus

Welcome to our class!

In this class, we will consider the following two central biological questions (the computational approaches needed to solve them are shown in parentheses):

  1. Weeks 1-3: Which Animal Gave Us SARS? (Evolutionary tree construction)
  2. Weeks 4-5: Was T. rex Just a Big Chicken? (Combinatorial Algorithms)

In Week 6, you will complete a Bioinformatics Application Challenge to apply evolutionary tree construction algorithms in order to determine the origin of the recent ebola outbreak in Africa.

As in previous courses, each of these two chapters is accompanied by a Bioinformatics Cartoon created by talented artist Randall Christopher and serving as a chapter header in the Specialization's bestselling print companion. You can find the first chapter's cartoon at the bottom of this message. What do stick bugs and bats have to do with deadly viruses? And how can bioinformatics be used to stop these viruses in their tracks? Start learning today and find out!

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Course Introduction

Molecular Evolution (Bioinformatics IV) The course covers the topics in bioinformatics IV and V in the context of nucleic acid evolution. It includes a full model simulation of a human genome and a complete program that simulates an entire human genome.Week 1 Week 2 Week 3 More C++ For C Programmers This course is for experienced C programmers who want to program in C++. The examples and exercises require a basic understanding of algorithms and object-oriented software.Module 1 Module 2 Module 3 Module 4 More C++ For C Programmers This course is for experienced C programmers who want to program in C++. The examples and exercises require a basic understanding of algorithms and object-oriented software.Module 1 Module 2 Module 3 Module 4 Networking and Extending This course will cover topics related to network protocols and technologies, including the common physical and logical connections involved in various protocols. We'll learn about packet protocols, packet filters, wireless communication, and many more topics. We'll also learn about network extenders and how to use them to extend the reachability and applicability of your programs.Module 1 Module 2 Module 3 Module 4 Networking Ess

Course Tag

Related Wiki Topic

Article Example
Molecular evolution The Society for Molecular Biology and Evolution publishes the journals "Molecular Biology and Evolution" and "Genome Biology and Evolution" and holds an annual international meeting. Other journals dedicated to molecular evolution include "Journal of Molecular Evolution" and "Molecular Phylogenetics and Evolution". Research in molecular evolution is also published in journals of genetics, molecular biology, genomics, systematics, and evolutionary biology.
Molecular evolution Depending on the relative importance assigned to the various forces of evolution, three perspectives provide evolutionary explanations for molecular evolution.
Molecular evolution Molecular evolution is the process of change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes. Major topics in molecular evolution concern the rates and impacts of single nucleotide changes, neutral evolution vs. natural selection, origins of new genes, the genetic nature of complex traits, the genetic basis of speciation, evolution of development, and ways that evolutionary forces influence genomic and phenotypic changes.
Journal of Molecular Evolution In 1999, under the new joint editorship of Martin Kreitman, Takashi Gojobori, and Giorgio Bernardi, the journal made explicit its focus on "the fundamental issues in molecular evolution", to the exclusion of molecular phylogenetics (the purview of several other molecular evolution journals, most significantly "Molecular Phylogenetics and Evolution"), except in cases that have "a special significance and impact".
Bioinformatics There are several large conferences that are concerned with bioinformatics. Some of the most notable examples are Intelligent Systems for Molecular Biology (ISMB), European Conference on Computational Biology (ECCB), and Research in Computational Molecular Biology (RECOMB).
Molecular evolution The field of molecular evolution came into its own in the 1960s and 1970s, following the rise of molecular biology. The advent of protein sequencing allowed molecular biologists to create phylogenies based on sequence comparison, and to use the differences between homologous sequences as a molecular clock to estimate the time since the last universal common ancestor. In the late 1960s, the neutral theory of molecular evolution provided a theoretical basis for the molecular clock, though both the clock and the neutral theory were controversial, since most evolutionary biologists held strongly to panselectionism, with natural selection as the only important cause of evolutionary change. After the 1970s, nucleic acid sequencing allowed molecular evolution to reach beyond proteins to highly conserved ribosomal RNA sequences, the foundation of a reconceptualization of the early history of life.
Molecular evolution Selectionist hypotheses argue that selection is the driving force of molecular evolution. While acknowledging that many mutations are neutral, selectionists attribute changes in the frequencies of neutral alleles to linkage disequilibrium with other loci that are under selection, rather than to random genetic drift. Biases in codon usage are usually explained with reference to the ability of even weak selection to shape molecular evolution.
Journal of Molecular Evolution The Journal of Molecular Evolution is a peer-reviewed scientific journal that covers molecular evolution. The journal is published by Springer and was established in 1971. The founding editor is Emile Zuckerkandl, who remained editor in chief until the late 1990s. In 1994, the journal became associated with the newly formed International Society of Molecular Evolution.
History of molecular evolution While evolutionary biologists were tentatively branching out into molecular biology, molecular biologists were rapidly turning their attention toward evolution.
Jotun Hein Hein's research interests are in molecular evolution, molecular population genetics and bioinformatics.
History of molecular evolution King and Jukes' paper, especially with the provocative title, was seen as a direct challenge to mainstream neo-Darwinism, and it brought molecular evolution and the neutral theory to the center of evolutionary biology. It provided a mechanism for the molecular clock and a theoretical basis for exploring deeper issues of molecular evolution, such as the relationship between rate of evolution and functional importance. The rise of the neutral theory marked synthesis of evolutionary biology and molecular biology—though an incomplete one.
History of molecular evolution With their work on firmer theoretical footing, in 1971 Emile Zuckerkandl and other molecular evolutionists founded the "Journal of Molecular Evolution".
History of molecular evolution The history of molecular evolution starts in the early 20th century with "comparative biochemistry", but the field of molecular evolution came into its own in the 1960s and 1970s, following the rise of molecular biology. The advent of protein sequencing allowed molecular biologists to create phylogenies based on sequence comparison, and to use the differences between homologous sequences as a molecular clock to estimate the time since the last common ancestor. In the late 1960s, the neutral theory of molecular evolution provided a theoretical basis for the molecular clock, though both the clock and the neutral theory were controversial, since most evolutionary biologists held strongly to panselectionism, with natural selection as the only important cause of evolutionary change. After the 1970s, nucleic acid sequencing allowed molecular evolution to reach beyond proteins to highly conserved ribosomal RNA sequences, the foundation of a reconceptualization of the early history of life.
Molecular evolution There are sometimes discordances between molecular and morphological evolution, which are reflected in molecular and morphological systematic studies, especially of bacteria, archaea and eukaryotic microbes. These discordances can be categorized as two types: (i) one morphology, multiple lineages (e.g. morphological convergence, cryptic species) and (ii) one lineage, multiple morphologies (e.g. phenotypic plasticity, multiple life-cycle stages). Neutral evolution possibly could explain the incongruences in some cases.
Molecular Biology and Evolution Molecular Biology and Evolution is a monthly peer-reviewed scientific journal published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. It publishes work in the intersection of molecular biology and evolutionary biology. The founding editors-in-chief were Walter Fitch and Masatoshi Nei; the present editor-in-chief is Sudhir Kumar.
European Bioinformatics Institute The European Bioinformatics Institute (EMBL-EBI) is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory (EMBL).
Pharmaceutical bioinformatics Whereas traditional bioinformatics is a wide subject it has a large focus on molecular biology, pharmaceutical bioinformatics more specifically targets chemical-biological interaction and exploratory focus of chemical and biological interactors using e.g. cheminformatics and chemometrics methods. Methods include, apart from many general bioinformatics methods, ligand-based modeling such as Quantitative structure–activity relationship (QSAR) and proteochemometrics, computer-aided molecular design, chembioinformatics databases, algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery.
Bioinformatics Over the past few decades, rapid developments in genomic and other molecular research technologies and developments in information technologies have combined to produce a tremendous amount of information related to molecular biology. Bioinformatics is the name given to these mathematical and computing approaches used to glean understanding of biological processes.
History of molecular evolution Though not directly related to molecular evolution, the mid-1960s also saw the rise of the gene-centered view of evolution, spurred by George C. Williams's "Adaptation and Natural Selection" (1966). Debate over units of selection, particularly the controversy over group selection, led to increased focus on individual genes (rather than whole organisms or populations) as the theoretical basis for evolution. However, the increased focus on genes did not mean a focus on molecular evolution; in fact, the adaptationism promoted by Williams and other evolutionary theories further marginalized the apparently non-adaptive changes studied by molecular evolutionists.
Molecular evolution The history of molecular evolution starts in the early 20th century with comparative biochemistry, and the use of "fingerprinting" methods such as immune assays, gel electrophoresis and paper chromatography in the 1950s to explore homologous proteins.