Phylogeny

12 Key excerpts on "Phylogeny"

• 

  No longer available |Learn more

  Cladistics (Method of Classifying Species of Organisms into Groups)

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

    (Publisher)

  ________________________ WORLD TECHNOLOGIES ________________________ Chapter- 7 Phylogenetics In biology, phylogenetics is the study of evolutionary relatedness among various groups of organisms (for example, species or populations), which is discovered through molecular sequencing data and morphological data matrices. The term phylogenetics is of Greek origin from the terms phyle/phylon (φυλή/φ ῦ λον), meaning tribe, race, and genetikos (γενετικός), meaning relative to birth from genesis (γένεσις, birth). Taxonomy, the classification, identification, and naming of organisms, has been richly informed by phylogenetics but remains methodologically and logically distinct. The fields overlap however in the science of phylogenetic systematics – often called cladism or cladistics – where only phylogenetic trees are used to delimit taxa, which represent groups of lineage-connected individuals. In biological systematics as a whole, phylogenetic analyses have become essential in researching the evolutionary tree of life. Construction of a phylogenetic tree Evolution is regarded as a branching process, whereby populations are altered over time and may speciate into separate branches, hybridize together, or terminate by extinction. This may be visualized in a phylogenetic tree. The problem posed by phylogenetics is that genetic data are only available for living taxa, and the fossil records (osteometric data) contains less data and more-ambiguous morphological characters. 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.

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Bioinformatics: A Swiss Perspective

  A Swiss Perspective

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

    (Publisher)

  Section III PHYLOGENETICS AND EVOLUTIONARY BIOINFORMATICS This page intentionally left blank This page intentionally left blank 285 Chapter 11 An Introduction to Phylogenetics and Its Molecular Aspects Gabriel Jîvasattha Bittar and Bernhard Pascal Sonderegger 1. Introduction In general terms, phylogenetics is the study of the relationships between evolving objects. The term derives from the Greek phylon (“race, tribe, (old) family”) and genos (“birth, origin”), gennêtikos (“related to gener-ation, to the genesis (of something)”). Phylogenetics is part biology and part information science. It is a discipline that helps to shed light on the ways in which biological objects (organisms, genes) have appeared and evolved. Evolutionary science has demonstrated that all living things have a common ancestry, but the root of the tree of life on this planet lies nearly 4 billion years in the past. Since then, evolution and phylogenesis have shaped a huge variety of biologi-cal objects. On the whole, the tree of life is becoming more complex over time. The process in which evolution tends to form more and more diverse forms of life, in spite of (or maybe because of ) catastrophic extinctions, is called cladogenesis (from the Greek kladon (“branch”)). In addition to this process, the life forms themselves generally tend to become more and more complex — a process called anagenesis (from the Greek ana - (“up, to the top”)). Phylogenetics incorporates both clado-genetics and anagenetics. The essence of the cladogenetic part of phylogenetics can be illus-trated by means of a simple graph. In Fig. 1, points C, D, and E — also called terminal nodes — are the present-time forms of an object capable of duplication and evolution. Some time ago, an ancestral form B bifur-cated into two diverging forms, ending in present-day forms D and E. An earlier ancestral form A had previously bifurcated into two diverging forms, resulting in the ancestral form B and the present-day form C.

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Bioinformatics

  • Andreas D. Baxevanis, Gary D. Bader, David S. Wishart, Andreas D. Baxevanis, Gary D. Bader, David S. Wishart(Authors)
  • 2020(Publication Date)
  • Wiley

    (Publisher)

  Darwin’s seminal work was the first to describe this mechanism for evolutionary change, and also championed the theory that evolutionary processes give rise to biodiversity. Biodiversity on Earth has previously been esti-mated to range widely, from 3 to 100 million species, while more recent numbers suggest that there are closer to a trillion living species, with only 1.9 million species actually named and only 1.6 million species cataloged in databases (Mora et al. 2011; Ruggiero et al. 2015; Loceya and Lennona 2016). Systematics is the study of the interrelationships of living things. How all these species are named and classified into higher order groups is a branch of science called taxonomy . There are many ways to group organisms that have been used in the past and will be discussed below. The focus of this chapter is phylogenetics – the field of systematics that focuses on evolution-ary relationships between organisms, groups of organisms (e.g. species or populations), or even the genes and proteins found within organisms. A “phylogenetic relationship” between entities such as species, genes, or proteins refers to how those entities shared a common ances-tor at some point in the past. Phylogenetic analyses always allow one to infer relationships. Bioinformatics, Fourth Edition. Edited by Andreas D. Baxevanis, Gary D. Bader, and David S. Wishart. © 2020 John Wiley & Sons, Inc. Published 2020 by John Wiley & Sons, Inc. Companion Website: www.wiley.com/go/baxevanis/Bioinformatics_4e 252 Molecular Evolution and Phylogenetic Analysis Phylogenetic analysis now commonly uses cladistics – a particular method of hypothesizing relationships among organisms, genes, or proteins. These analyses are based on branching patterns depicted using tree-like representations quite similar to human family trees and are constructed based on similarities in traits or characters .

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  The Princeton Guide to Evolution

  • David A. Baum, Douglas J. Futuyma, Hopi E. Hoekstra, Richard E. Lenski, Allen J. Moore, Catherine L. Peichel, Dolph Schluter, Michael C. Whitlock, David A. Baum, Douglas J. Futuyma, Hopi E. Hoekstra, Richard E. Lenski, Allen J. Moore, Catherine L. Peichel, Dolph Schluter, Michael C. Whitlock(Authors)
  • 2013(Publication Date)
  • Princeton University Press

    (Publisher)

  All organisms on earth share common ancestry; we are related to every species that has ever existed. Evolutionary biologists since Darwin have sought to infer a “tree of life,” a phylogenetic tree showing how all species are related to one another. The concept of Phylogeny as the evolutionary history of organisms—and phylogenetic trees as a depiction of that history—is central to evolutionary biology. Phylogenies form the basis for our understanding of relationships among organisms, and they are key tools of modern evolutionary research; however, phylogenetic trees are frequently misinterpreted because of fundamental misconceptions about what trees can and cannot tell us. In particular, people frequently misinterpret trees by reading trees “laterally” from one extant species to the next. This tendency results partly from mistakenly thinking of evolution as a “ladder of progress.” Ultimately, a well-informed interpretation of phylogenetic trees goes hand in hand with a clear understanding of the process of evolution.

  GLOSSARY

  Ancestral State Reconstruction. A procedure that uses a Phylogeny as well as character data from extant species to infer likely ancestral character states.

  Character State. Alternative states for a given biological character (e.g., brown, blue, hazel are character states of the character eye color; A, C, G, or T are character states of the character corresponding to base position 12 in the actin gene).

  Chronogram. A phylogenetic tree with branch lengths scaled to represent time (related to phylogram, a tree in which branch lengths are scaled to the amount of character evolution).

  Cladogram. An unscaled phylogenetic tree that shows relationships among organisms, but in which branch lengths are meaningless. The key information retained in a cladogram is topology, which refers to the composition of clades/monophyletic groups and how they are related to one another.

  Derived

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  The Evolution of Man — Volume 1

  • Ernst Haeckel(Author)
  • 2004(Publication Date)
  • Perlego

    (Publisher)

  The story of the evolution of man, as it has hitherto been expounded to medical students, has usually been confined to embryology—more correctly, ontogeny—or the science of the development of the individual human organism. But this is really only the first part of our task, the first half of the story of the evolution of man in that wider sense in which we understand it here. We must add as the second half—as another and not less important and interesting branch of the science of the evolution of the human stem—Phylogeny: this may be described as the science of the evolution of the various animal forms from which the human organism has been developed in the course of countless ages. Everybody now knows of the great scientific activity that was occasioned by the publication of Darwin's Origin of Species in 1859. The chief direct consequence of this publication was to provoke a fresh inquiry into the origin of the human race, and this has proved beyond question our gradual evolution from the lower species. We give the name of "Phylogeny" to the science which describes this ascent of man from the lower ranks of the animal world. The chief source that it draws upon for facts is "Ontogeny," or embryology, the science of the development of the individual organism. Moreover, it derives a good deal of support from paleontology, or the science of fossil remains, and even more from comparative anatomy, or morphology.

  These two branches of our science—on the one side ontogeny or embryology, and on the other Phylogeny, or the science of race-evolution—are most vitally connected. The one cannot be understood without the other. It is only when the two branches fully co-operate and supplement each other that "Biogeny" (or the science of the genesis of life in the widest sense) attains to the rank of a philosophic science. The connection between them is not external and superficial, but profound, intrinsic, and causal. This is a discovery made by recent research, and it is most clearly and correctly expressed in the comprehensive law which I have called "the fundamental law of organic evolution," or "the fundamental law of biogeny." This general law, to which we shall find ourselves constantly recurring, and on the recognition of which depends one's whole insight into the story of evolution, may be briefly expressed in the phrase: "The history of the foetus is a recapitulation of the history of the race"; or, in other words, "Ontogeny is a recapitulation of Phylogeny." It may be more fully stated as follows: The series of forms through which the individual organism passes during its development from the ovum to the complete bodily structure is a brief, condensed repetition of the long series of forms which the animal ancestors of the said organism, or the ancestral forms of the species, have passed through from the earliest period of organic life down to the present day.

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  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.

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  Biology of Aging

  • Roger B. McDonald(Author)
  • 2019(Publication Date)
  • Garland Science

    (Publisher)

  Although morphological classification systems are being replaced by phylogenetic systems, the taxonomic names developed by Linnaeus are still widely used. After the rediscovery and ultimate understanding of Mendel’s principles of genetics, biologists began questioning whether evolution actually reflected an orderly procession of life from low to high complexity. Pressure to use an alternative form of classification grew even stronger with the discovery that the structure of DNA was identical in all organisms and that many genes found in “lower” life forms were identical to those found in “higher” animals. These findings provided solid and conclusive evidence that all life descended from a single common ancestor or, at most, a few common ancestors. In addition, evolutionists were finding that morphological complexity was a poor descriptor of evolutionary history for a species. Species were only as complex as they needed to be for survival in their environment. Thus, complexity was related more closely to the species’ ability to survive in its environment than to a human definition of purpose. Advancement in the biological sciences during the mid- to late-twentieth century led to the development of a classification system based on Phylogeny rather than on morphology. Phylogeny is the evolutionary sequence of events involved in the development of a species or of groups of organisms. Modern phylogenetics uses a combination of factors and techniques to establish the evolutionary relationships among species. These include morphological characteristics, DNA sequences, ecological data, and mathematical algorithms to predict likely gene relationships. Phylogenetics does not consider one species more advanced than another

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  The Comparative Approach in Evolutionary Anthropology and Biology

  • Charles L. Nunn(Author)
  • 2011(Publication Date)
  • University of Chicago Press

    (Publisher)

  2 Basic Phylogenetic Concepts and “Tree Thinking”

  One of the most significant breakthroughs in biology was the realization that lineages of organisms can be represented with a branching tree structure. Because languages, societies, and organisms all descend in a hierarchical fashion from ancestors, trees are a fundamental way of understanding the connections among the individual data points in a comparative study. Geography is also important, especially for situations in which adjacent locations have similar ecological conditions, or when traits can spread horizontally, such as “loanwords” among languages.

  A principal theme of this book is that knowing the historical relationships among the organisms or populations in a comparative dataset can generate a richer understanding of variation. While this point might seem obvious, many anthropological, primatological, and linguistic studies fail to make use of phylogenetic information. At an even more basic level, a remarkable number of biologists and evolutionary anthropologists fail to appreciate the most basic concepts about phylogenies. Many readers of this book are likely to assume that they already know how to read a Phylogeny and so might be tempted to skip this chapter. Before doing so, I recommend taking the “Tree-Thinking Challenge,” published as part of a Science article on the need for increased phylogenetic perspective in biological research (Baum et al. 2005) and linked through AnthroTree (AnthroTree 2.1). It is possible to climb the “phylogenetics learning curve” simply by taking the test and reading the brief explanations to the questions.

  In this book, I am concerned primarily with making use of phylogenetic information in comparative research rather than with creating phylogenies. Few recent books, most dating from the 1990s, have been devoted to using phylogenetic trees in comparative research (Harvey and Pagel 1991; Harvey et al. 1995; Martins 1996a). This is surprising, given the publication of many new and more powerful approaches for investigating comparative data since the publication of these books. In contrast, many recent books have been devoted to building phylogenies (Page and Holmes 1998; Nei and Kumar 2000; Felsenstein 2004; Hall 2008). Thus, I refer readers seeking more information to the books on phylogenetics just cited, and I limit coverage of tree-building techniques and concepts to the basics in this chapter. I also use jargon associated with phylogenetics on a “need-to–know basis” relative to the topics covered later in the book, as a full listing of terms is not essential (and phylogeneticists have created a dense jungle of terms).

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Phylogenetics

  • Ibrokhim Y. Abdurakhmonov(Author)
  • 2017(Publication Date)
  • IntechOpen

    (Publisher)

  Such a classification recalls a scenario like ancestor-descendent relationships among taxa (Phylogeny), which result in a scheme describing an evolutionary relationship that could not be subject to critical analysis. Recently, modern phylogenetic science captures, as empirically as possible, the relatedness among similar taxa using the most orderly manner for mapping the path of evolution that leads to and represents the true ancestry relating the upstream organisms. The resultant classification must be reasonably and objectively assumed by world -wide biologists, undoubtedly. In this way, groups of species or its populations are essentially related by a set of both, morphological and molecular characteristics but, more importantly yet, these should be matched by properties such as its ecological abilities. Firstly, phylogenetic studies have been proven to be of utility, of course, but in a research-ori -ented framework. In this way, a simple data research can provide guidelines to find gaps and strengthen interpretations to ensure management affirmations. So, multi-locus phylogenies can be used to infer the species tree whose nodes represent the actual separation between species, thus providing essential information about their evolutionary history or helping ana -lyzes of species delimitation, gene flow, and genetic differentiation within species [17]. As an example, now adequate markers are available by extracting intron information from genomes of human, chimpanzee, macaque, cow, and dog (three mammalian orders) searching for the Phylogenetics for Wildlife Conservation http://dx.doi.org/10.5772/intechopen.69240 29 ENSEMBL database. This analysis led to a final list of 224 intron markers randomly distrib -uted along the genome for six mammals species, which can be useful to gather genetic mark -ers with unambiguous phylogenetic signals (see [17] for details and design) ( Figure 1 ).

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Phylogenies in Ecology

  A Guide to Concepts and Methods

  • Marc W. Cadotte, T. Jonathan Davies(Authors)
  • 2016(Publication Date)
  • Princeton University Press

    (Publisher)

  As independent areas of research, ecological and evolutionary studies have provided profound insights into the formation and function of bio-logical systems. For example, ecologists have developed predictions about species coexistence based on the ratios of limiting resources (Tilman 1982) and several theories of macroecology explain large-scale diversity patterns (Blackburn and Gaston 2006). Despite, or even because of this early history, researchers today are working in an era of synthesis, where Moore’s two great forces are now part of unified explanations in ecology (Ricklefs 2007). Evolutionary history has long informed our view of the world, and its consideration can be traced back in the scientific literature at least as far as Charles Darwin’s On the Origin of Species (Darwin 1859). More recently, we have been witness to a rapid development of phylo-genetic methods allowing phylogenetically informed comparisons of traits among groups of species (Felsenstein 1985, Harvey and Pagel 1991). Critically, concomitant advances in tech-nologies have provided us with the raw material required for these new approaches—molec-ular sequences and phylogenetic trees. Interest in using phylogenetic information to evaluate mechanisms of community assembly and coexistence (Webb 2000) and niche conservatism (Holt 1996, Wiens and Graham 2005) increased dramatically as phylogenetic information for entire regions, clades, and communities has become readily available (fig. 1.1). 2 • CHAPTER 1 Here we briefly review the history of the use of phylogenetics in ecology, starting with early attempts to classify the diversity of life and the development of evolutionary theory, through the rise of the comparative method, and finally to the emergence of ecological phylogenetics or ecophylogenetics .

  Sign up to read

  Learn more about book
• 

  eBook - PDF

  Logic, Methodology and Philosophy of Science VIII

  • J.E. Fenstad, I.T. Frolov, R. Hilpinen(Authors)
  • 1989(Publication Date)
  • North Holland

    (Publisher)

  488 R. LOTHER If we understand the “phylogenetic tree” as the universal ideal repro- duction of life’s history on earth at the level of populations and species, then the phylogenetic (cladistic) system represents its basic structure, seen from the present time. As HENNIG (1950: p. 278) remarked, the phylogenetic tree of organisms-conceived as a diagram in which their phylogenetic (cladistic) relationships are related to their similarities in each conceivable direction - is a multidimensional structure which can- not be represented completely figuratively by a single picture. Therefore different projections of this polystructure are necessary for further cogni- tion. These include -the classification systems related to different strata of phenomena, to -the classification systems related to different temporal horizons of the - the representations of the phylogenetic tree which are expressed by the phenetic, patristic, and cladistic relationships; past as cross-sections across the phylogenetic tree; classification systems related to different levels of phenomena. This totality is the conceptual network for catching the spatiotemporal diversity of the world of organisms. The phylogenetic (cladistic) classifica- tion system is the general reference system of the mental mastering of the organismic diversity sub specie evolutionis. The factors, moving forces, and regularities of the historical develop- ment of life, of its evolution, are the subject-matter of the biological theory of evolution. The evolutionary theory is founded on the study of the present processes in order to explain the ideally reconstructed course of evolution. It answers the question how evolution works. Since Dar- win’s On the Origin of Species by Means of Natural Selection (1859) it has passed through various stages of development. With Th. Dobzhansky’s Genetics and the Origin of Species (1937) began the stage of the Synthetic Theory of Evolution, of the synthesis of Darwinism and genetics.

  Sign up to read

  Learn more about book
• 

  eBook - ePub

  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

  Sign up to read

  Learn more about book