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12.4: Introduction to Phylogenetic Trees - Biology

12.4: Introduction to Phylogenetic Trees - Biology


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What you’ll learn to do: Read and analyze a phylogenetic tree that documents evolutionary relationships

In scientific terms, the evolutionary history and relationship of an organism or group of organisms is called phylogeny. Phylogeny describes the relationships of an organism, such as from which organisms it is thought to have evolved, to which species it is most closely related, and so forth.

Phylogenetic relationships provide information on shared ancestry but not necessarily on how organisms are similar or different. In other words, a “tree of life” can be constructed to illustrate when different organisms evolved and to show the relationships among different organisms (Figure 1).

Figure 1. This phylogenetic tree was constructed by microbiologist Carl Woese (See inset below) using genetic relationships. The tree shows the separation of living organisms into three domains: Bacteria, Archaea, and Eukarya. Bacteria and Archaea are organisms without a nucleus or other organelles surrounded by a membrane and, therefore, are prokaryotes. (credit: modification of work by Eric Gaba)


Baum and Smith, both professors evolutionary biology and researchers in the field of systematics, present this highly accessible introduction to phylogenetics and its importance in modern biology. Ever since Darwin, the evolutionary histories of organisms have been portrayed in the form of branching trees or “phylogenies.” However, the broad significance of the phylogenetic trees has come to be appreciated only quite recently. Phylogenetics has myriad applications in biology, from discovering the features present in ancestral organisms, to finding the sources of invasive species and infectious diseases, to identifying our closest living (and extinct) hominid relatives. Taking a conceptual approach, Tree Thinking introduces readers to the interpretation of phylogenetic trees, how these trees can be reconstructed, and how they can be used to answer biological questions. Examples and vivid metaphors are incorporated throughout, and each chapter concludes with a set

باوم و اسمیت، هر دو از استادان زیست شناسی تکاملی و محققان در زمینه سیستماتیک، در حال حاضر این مقدمه بسیار در دسترس به فیلوژنتیک و اهمیت آن در زیست شناسی مدرن. از زمانی که داروین، تاریخ تکاملی ارگانیسم ها در قالب درختان انشعاب و یا به تصویر کشیده شده است “؛. فیلوژنیها”؛ با این حال، اهمیت گسترده ای از درخت فیلوژنتیک آمده است به قدردانی می شود در این اواخر. فیلوژنتیک دارای کاربردهای بی شمار در زیست شناسی، از کشف ویژگی های موجود در موجودات اجدادی، به پیدا کردن منابع از گونه های مهاجم و بیماری های عفونی، به شناسایی نزدیکترین زندگی (و منقرض شده) ما بستگان انسان. با توجه به رویکرد مفهومی، درخت تفکر معرفی خوانندگان به تفسیر درخت فیلوژنتیک، چگونه این درختان را می توان بازسازی، و چگونه آنها می توان برای پاسخ به سوالات بیولوژیکی. مثال ها و استعارات ملموس در سراسر گنجانیده شده است، و هر فصل با یک مجموعه

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12.4: Introduction to Phylogenetic Trees - Biology

Like family trees, phylogenetic trees represent patterns of ancestry. However, while families have the opportunity to record their own history as it happens, evolutionary lineages do not — species in nature do not come with pieces of paper showing their family histories. Instead, biologists must reconstruct those histories by collecting and analyzing evidence, which they use to form a hypothesis about how the organisms are related — a phylogeny.

In order to construct the vertebrate phylogeny, we begin by examining representatives of each lineage to learn about their basic morphology, whether or not the lineage has vertebrae, a bony skeleton, four limbs, an amniotic egg, etc.

Using shared derived characters
Our goal is to find evidence that will help us group organisms into less and less inclusive clades. Specifically, we are interested in shared derived characters. A shared character is one that two lineages have in common, and a derived character is one that evolved in the lineage leading up to a clade and that sets members of that clade apart from other individuals.

Shared derived characters can be used to group organisms into clades. For example, amphibians, turtles, lizards, snakes, crocodiles, birds and mammals all have, or historically had, four limbs. If you look at a modern snake you might not see obvious limbs, but fossils show that ancient snakes did have limbs, and some modern snakes actually do retain rudimentary limbs. Four limbs is a shared derived character inherited from a common ancestor that helps set apart this particular clade of vertebrates.

However, the presence of four limbs is not useful for determining relationships within the clade in green above, since all lineages in the clade have that character. To determine the relationships in that clade, we would need to examine other characters that vary across the lineages in the clade.


Tree Thinking: An Introduction to Phylogenetic Biology

Read and study old-school with our bound texts.

Baum and Smith, both professors evolutionary biology and researchers in the field of systematics, present this highly accessible introduction to phylogenetics and its importance in modern biology. Ever since Darwin, the evolutionary histories of organisms have been portrayed in the form of branching trees or “phylogenies.” However, the broad significance of the phylogenetic trees has come to be appreciated only quite recently. Phylogenetics has myriad applications in biology, from discovering the features present in ancestral organisms, to finding the sources of invasive species and infectious diseases, to identifying our closest living (and extinct) hominid relatives. Taking a conceptual approach, Tree Thinking introduces readers to the interpretation of phylogenetic trees, how these trees can be reconstructed, and how they can be used to answer biological questions. Examples and vivid metaphors are incorporated throughout, and each chapter concludes with a set of problems, valuable for both students and teachers. Tree Thinking is must-have textbook for any student seeking a solid foundation in this fundamental area of evolutionary biology.

“Phylogenetics has had a revolutionary impact on biology in the last few decades, but few books convey the power and beauty of the field at an introductory level like this one does. It will help fill a long empty niche in undergraduate curricula and serve as a good prerequisite to more technical treatments at the graduate level.” —Michael Sanderson, University of Arizona

“This book is perfect for the kind of phylogeny course that we should be teaching everywhere.”  —Michael J. Donoghue, Sterling Professor of Ecology and Evolutionary Biology, Yale University

“We can’t expect students and the general public to understand the big idea of evolution—common ancestry—if we neglect to teach them the basic skills necessary to understand and interpret evolutionary trees. Tree Thinking is an exceptional resource for scientists, graduate students, and science educators.” —Louise Mead, Education Director at BEACON Center for the Study of Evolution in Action, Michigan State University

“Baum and Smith’s Tree Thinking is an admirably clear introduction to building and interpreting trees.” —Mark Pagel, FRS, Professor of Evolutionary Biology, University of Reading

“Phylogenetic analysis has become a fundamental element of 21st century biology, impacting all disciplines from molecular biology to ecosystem structure, from population genetics to the Tree of Life. Tree Thinking will help educators and students develop the skills crucial to understanding the evolutionary concepts underlying modern biology.” —Richard Olmstead, Professor of Biology and Herbarium Curator, University of Washington

“Tree thinking is not intuitive it doesn’t come easily to most people. Yet it’s an essential tool for understanding how organisms—and their traits—evolve. Baum and Smith have provided a helpful guide to learning how to think like an evolutionary biologist. Their treatment is accessible, balanced, and well informed.” —James Hanken, Alexander Agassiz Professor of Zoology, Curator in Herpetology, and Director, Museum of Comparative Zoology, Harvard University

“Baum and Smith have produced a book that hits its target squarely. Tree thinking will be a critical tool in the arsenal of those of us who train the next generation of evolutionary biologists.” —Jack Sullivan, President of the Society of Systematic Biologists, and Professor of Biology, University of Idaho

“A timely and well-written primer. Highly recommended for anyone interested in taking a phylogenetic approach to study evolution.” —Jonathan B. Losos, Curator in Herpetology, and Monique and Philip Lehner Professor for the Study of Latin America, Harvard University

“Kudos to Baum and Smith, two highly accomplished phylogeneticists, for this clear and concise book, which is truly a much needed text for the field of phylogenetic biology. Both plant and animal examples are used throughout to show how an evolutionary tree depicts the relationships among organisms through time. Tree Thinking will be a required text for when I next teach Phylogenetic Plant Systematics.” —Kathleen Pryer, Professor of Biology, Duke University

"Where was this book when I taught my first phylogentics course 10 years ago?! But better late than never. Baum and Smith have provided the first general text for teaching a difficult to grasp subject, what is a phylogenetic tree and how best to infer one, in a non-technical framework." —Sydney Cameron, Professor of Biology, University of Illinois

Tree Thinking: An Introduction to Phylogenetic Biology

David A. Baum Stacey D. Smith


Getting Started

Google search for GenBank and click on the result for GenBank Home (http://www.ncbi.nlm.nih.gov/genbank/).

Use the dropdown next to the word GenBank to change from default Nucleotide and select Gene .

Type RuBisCO large subunit in the entry box to the right of dropdown and click Search .

Select the link rbcL for the RuBisCO large subunit for a given species – here, we will use Zea mays.

Click on Genomic regions, transcripts, and products in the table of contents.

Copy and paste the sequence of rbcL gene from Zea mays (Figure 1).

After pasting into Notepad, leave the prompt sign > and delete text before the DNA sequence, then replace deleted text with Corn, the common name for Zea mays .

Click File then Save . A Save As dialog box will appear. In the Save as type : drop down choose All files (*.*) and save this file as “corn.fasta”.

We now have the rbcL gene sequence for one species. We need to collect sequences for nine other species for comparison in MEGA (see Table 1). In addition, we will use Euglena viridis as our outgroup. Repeat the procedure with each species listed below by typing the GenBank Gene ID into the search box. Save each sequence in a separate file as suggested in Table 1.

Paste the sequence data into a Notepad (PC) or Texteditor (Mac/Linux). To find Notepad on a PC with Windows, go to the Start Menu, All Programs, then click Accessories and you should see Notepad.

Paste the sequence data into a Notepad (PC) or Texteditor (Mac/Linux). To find Notepad on a PC with Windows, go to the Start Menu, All Programs, then click Accessories and you should see Notepad.

Common Name . GenBank ID . File Name .
Corn 845212 corn.fasta
Thale cress 844754 thalecress.fasta
Rice 4126887 rice.fasta
Tobacco 800513 tobacco.fasta
Potato 4099985 potato.fasta
Liverwort 2702554 liverwort.fasta
Sunflower 4055709 sunflower.fasta
Grape 4025045 grape.fasta
Cucumber 3429289 cucumber.fasta
Spinach 2715621 spinach.fasta
Common Name . GenBank ID . File Name .
Corn 845212 corn.fasta
Thale cress 844754 thalecress.fasta
Rice 4126887 rice.fasta
Tobacco 800513 tobacco.fasta
Potato 4099985 potato.fasta
Liverwort 2702554 liverwort.fasta
Sunflower 4055709 sunflower.fasta
Grape 4025045 grape.fasta
Cucumber 3429289 cucumber.fasta
Spinach 2715621 spinach.fasta

Tree Thinking: An Introduction to Phylogenetic Biology

Baum and Smith, both professors evolutionary biology and researchers in the field of systematics, present this highly accessible introduction to phylogenetics and its importance in modern biology. Ever since Darwin, the evolutionary histories of organisms have been portrayed in the form of branching trees or “phylogenies.” However, the broad significance of the phylogenetic trees has come to be appreciated only quite recently. Phylogenetics has myriad applications in biology, from discovering the features present in ancestral organisms, to finding the sources of invasive species and infectious diseases, to identifying our closest living (and extinct) hominid relatives.

Taking a conceptual approach, Tree Thinking introduces readers to the interpretation of phylogenetic trees, how these trees can be reconstructed, and how they can be used to answer biological questions. Examples and vivid metaphors are incorporated throughout, and each chapter concludes with a set of problems, valuable for both students and teachers. Tree Thinking is must-have textbook for any student seeking a solid foundation in this fundamental area of evolutionary biology.


Watch the video: Reading u0026 producing phylogenetic trees: introduction (February 2023).