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Creating Phylogenetic Trees from DNA Sequences: Answer Key and Comprehensive Guide
Introduction:
Unlocking the secrets of evolutionary relationships is a fascinating journey, and phylogenetic trees are the key. These branching diagrams visually represent the evolutionary history of organisms, showcasing how species are related through common ancestors. If you're struggling to build accurate phylogenetic trees from DNA sequences, you've come to the right place. This comprehensive guide not only provides an "answer key" approach to common challenges but also offers a step-by-step understanding of the process, equipping you with the skills to confidently analyze your own data. We will explore various methods, discuss potential pitfalls, and offer practical tips to ensure accuracy and reliability in your phylogenetic analyses.
Understanding the Fundamentals: DNA Sequences and Phylogenetic Inference
Before diving into the practical application, let's solidify the underlying principles. Phylogenetic trees are constructed based on the principle of shared ancestry. Organisms with more similar DNA sequences are generally considered to be more closely related, having diverged more recently from a common ancestor. The differences in DNA sequences, specifically mutations (insertions, deletions, substitutions), provide the raw data for building these trees.
Types of Data Used:
Nuclear DNA: Provides a broader evolutionary perspective, useful for comparing distantly related species.
Mitochondrial DNA (mtDNA): Evolves relatively quickly, ideal for resolving relationships within closely related species or populations.
Chloroplast DNA (cpDNA): Similar to mtDNA, commonly used in plant phylogenetics.
Choosing the Right Method:
Several methods exist for constructing phylogenetic trees, each with its own strengths and limitations. The optimal method depends on the specific dataset and the research question. Some commonly used methods include:
Neighbor-Joining: A relatively fast and simple method, suitable for large datasets.
Maximum Parsimony: Seeks the tree that requires the fewest evolutionary changes (mutations) to explain the observed data.
Maximum Likelihood: Estimates the probability of observing the data given a particular tree and model of evolution.
Bayesian Inference: Uses Bayesian statistics to infer the probability of different trees, considering the prior probabilities of different evolutionary models.
A Step-by-Step Guide to Creating Phylogenetic Trees
This section outlines the process of creating a phylogenetic tree using DNA sequence data. We'll use a simplified example to illustrate the key steps. Remember that real-world analyses often involve more complex datasets and require specialized software.
Step 1: Data Acquisition and Alignment: Obtain your DNA sequences (e.g., from GenBank). Use bioinformatics tools like ClustalW or MAFFT to align the sequences, ensuring that homologous positions are correctly matched. Accurate alignment is crucial for reliable tree construction.
Step 2: Choosing a Phylogenetic Method: Select a suitable method based on your dataset size, the evolutionary relationships you wish to resolve, and computational resources.
Step 3: Tree Construction using Software: Utilize software packages like MEGA X, PhyML, MrBayes, or BEAST to construct your phylogenetic tree. These programs will perform the chosen phylogenetic method on the aligned DNA sequences.
Step 4: Tree Evaluation and Interpretation: Assess the robustness of your tree using bootstrap analysis or posterior probabilities. These values indicate the confidence level in the branching patterns of the tree. Interpret the tree's topology (branching pattern) to understand the evolutionary relationships among the species.
Troubleshooting Common Challenges
Creating phylogenetic trees isn't always straightforward. Here are some common pitfalls and their solutions:
Poor sequence alignment: Inaccurate alignment leads to erroneous phylogenetic inferences. Careful manual curation and the use of multiple alignment algorithms can help mitigate this.
Long branch attraction: Distantly related sequences with rapid evolution can appear more closely related than they actually are. Addressing this requires careful method selection and potentially incorporating rate heterogeneity models.
Homoplasy: Convergent evolution or reversals can lead to misleading relationships. Sophisticated phylogenetic methods are designed to account for this phenomenon.
Interpreting Your Phylogenetic Tree: An Answer Key to Common Questions
Once you have your phylogenetic tree, interpreting it is key. The branching pattern reveals evolutionary relationships. Branches represent lineages, nodes represent common ancestors, and branch lengths can sometimes indicate the amount of evolutionary change. Remember, phylogenetic trees are hypotheses, and their accuracy depends on the quality of the data and the chosen methodology.
Conclusion
Creating phylogenetic trees from DNA sequences is a powerful tool for understanding evolutionary history. This guide has provided a comprehensive overview of the process, from data acquisition and alignment to tree construction and interpretation. While challenges exist, understanding the underlying principles and utilizing appropriate software can lead to accurate and insightful phylogenetic analyses. Remember to critically evaluate your results, consider alternative methods, and consult relevant literature for best practice in your specific research area.
FAQs:
1. What software is best for creating phylogenetic trees? Several excellent options exist, including MEGA X, PhyML, MrBayes, and BEAST. The best choice depends on your data size, familiarity with the software, and the complexity of the analysis.
2. How do I interpret branch lengths in a phylogenetic tree? Branch lengths often represent the amount of evolutionary change (e.g., number of nucleotide substitutions). However, this interpretation depends on the chosen method and the underlying model of evolution. Some trees might display branch lengths that are not proportional to evolutionary time.
3. What is bootstrap support, and why is it important? Bootstrap analysis assesses the robustness of tree branches by repeatedly resampling the data and reconstructing the tree. Higher bootstrap values (typically above 70%) indicate greater confidence in the particular branching pattern.
4. Can I use phylogenetic trees to infer evolutionary timescales? While phylogenetic trees show evolutionary relationships, dating them requires additional information such as fossil calibrations or molecular clocks. These methods are used to estimate the time elapsed along each branch.
5. How can I improve the accuracy of my phylogenetic analysis? Consider using multiple alignment algorithms, testing various phylogenetic methods, incorporating rate heterogeneity models, and carefully evaluating the results using appropriate statistical support values (e.g., bootstrap values, posterior probabilities). Remember to consider potential sources of error, such as homoplasy and long branch attraction.
| creating phylogenetic trees from dna sequences answer key: Statistics and Truth Calyampudi Radhakrishna Rao, 1997 Written by one of the top most statisticians with experience in diverse fields of applications of statistics, the book deals with the philosophical and methodological aspects of information technology, collection and analysis of data to provide insight into a problem, whether it is scientific research, policy making by government or decision making in our daily lives.The author dispels the doubts that chance is an expression of our ignorance which makes accurate prediction impossible and illustrates how our thinking has changed with quantification of uncertainty by showing that chance is no longer the obstructor but a way of expressing our knowledge. Indeed, chance can create and help in the investigation of truth. It is eloquently demonstrated with numerous examples of applications that statistics is the science, technology and art of extracting information from data and is based on a study of the laws of chance. It is highlighted how statistical ideas played a vital role in scientific and other investigations even before statistics was recognized as a separate discipline and how statistics is now evolving as a versatile, powerful and inevitable tool in diverse fields of human endeavor such as literature, legal matters, industry, archaeology and medicine.Use of statistics to the layman in improving the quality of life through wise decision making is emphasized. |
| creating phylogenetic trees from dna sequences answer key: Concepts of Biology Samantha Fowler, Rebecca Roush, James Wise, 2023-05-12 Black & white print. Concepts of Biology is designed for the typical introductory biology course for nonmajors, covering standard scope and sequence requirements. The text includes interesting applications and conveys the major themes of biology, with content that is meaningful and easy to understand. The book is designed to demonstrate biology concepts and to promote scientific literacy. |
| creating phylogenetic trees from dna sequences answer key: Biology for AP ® Courses Julianne Zedalis, John Eggebrecht, 2017-10-16 Biology for AP® courses covers the scope and sequence requirements of a typical two-semester Advanced Placement® biology course. The text provides comprehensive coverage of foundational research and core biology concepts through an evolutionary lens. Biology for AP® Courses was designed to meet and exceed the requirements of the College Board’s AP® Biology framework while allowing significant flexibility for instructors. Each section of the book includes an introduction based on the AP® curriculum and includes rich features that engage students in scientific practice and AP® test preparation; it also highlights careers and research opportunities in biological sciences. |
| creating phylogenetic trees from dna sequences answer key: Molecular Evolution Roderick D.M. Page, Edward C. Holmes, 2009-07-14 The study of evolution at the molecular level has given the subject of evolutionary biology a new significance. Phylogenetic 'trees' of gene sequences are a powerful tool for recovering evolutionary relationships among species, and can be used to answer a broad range of evolutionary and ecological questions. They are also beginning to permeate the medical sciences. In this book, the authors approach the study of molecular evolution with the phylogenetic tree as a central metaphor. This will equip students and professionals with the ability to see both the evolutionary relevance of molecular data, and the significance evolutionary theory has for molecular studies. The book is accessible yet sufficiently detailed and explicit so that the student can learn the mechanics of the procedures discussed. The book is intended for senior undergraduate and graduate students taking courses in molecular evolution/phylogenetic reconstruction. It will also be a useful supplement for students taking wider courses in evolution, as well as a valuable resource for professionals. First student textbook of phylogenetic reconstruction which uses the tree as a central metaphor of evolution. Chapter summaries and annotated suggestions for further reading. Worked examples facilitate understanding of some of the more complex issues. Emphasis on clarity and accessibility. |
| creating phylogenetic trees from dna sequences answer key: Elementary Geology Edward Hitchcock, 1847 |
| creating phylogenetic trees from dna sequences answer key: Anthropological Genetics Michael H. Crawford, 2007 Volume detailing the effects of the molecular revolution on anthropological genetics and how it redefined the field. |
| creating phylogenetic trees from dna sequences answer key: Sequence — Evolution — Function Eugene V. Koonin, Michael Galperin, 2013-06-29 Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the digital divide between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics. |
| creating phylogenetic trees from dna sequences answer key: Tree Thinking: An Introduction to Phylogenetic Biology David A. Baum, Stacey D. Smith, 2012-08-10 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. |
| creating phylogenetic trees from dna sequences answer key: Bioinformatics and Functional Genomics Jonathan Pevsner, 2005-03-04 Wiley is proud to announce the publication of the first ever broad-based textbook introduction to Bioinformatics and Functional Genomics by a trained biologist, experienced researcher, and award-winning instructor. In this new text, author Jonathan Pevsner, winner of the 2001 Johns Hopkins University Teacher of the Year award, explains problem-solving using bioinformatic approaches using real examples such as breast cancer, HIV-1, and retinal-binding protein throughout. His book includes 375 figures and over 170 tables. Each chapter includes: Problems, discussion of Pitfalls, Boxes explaining key techniques and math/stats principles, Summary, Recommended Reading list, and URLs for freely available software. The text is suitable for professionals and students at every level, including those with little to no background in computer science. |
| creating phylogenetic trees from dna sequences answer key: Inferring Phylogenies Joseph Felsenstein, 2004-01 Phylogenies, or evolutionary trees, are the basic structures necessary to think about and analyze differences between species. Statistical, computational, and algorithmic work in this field has been ongoing for four decades now, and there have been great advances in understanding. Yet no book has summarized this work. Inferring Phylogenies does just that in a single, compact volume. Phylogenies are inferred with various kinds of data. This book concentrates on some of the central ones: discretely coded characters, molecular sequences, gene frequencies, and quantitative traits. Also covered are restriction sites, RAPDs, and microsatellites. |
| creating phylogenetic trees from dna sequences answer key: Analysis of Phylogenetics and Evolution with R Emmanuel Paradis, 2006-11-25 This book integrates a wide variety of data analysis methods into a single and flexible interface: the R language. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters. |
| creating phylogenetic trees from dna sequences answer key: Computational Molecular Evolution Ziheng Yang, 2006-10-05 This book describes the models, methods and algorithms that are most useful for analysing the ever-increasing supply of molecular sequence data, with a view to furthering our understanding of the evolution of genes and genomes. |
| creating phylogenetic trees from dna sequences answer key: Biological Sequence Analysis Richard Durbin, 1998-04-23 Presents up-to-date computer methods for analysing DNA, RNA and protein sequences. |
| creating phylogenetic trees from dna sequences answer key: Molecular Markers, Natural History and Evolution J. C. Avise, 2012-12-06 Molecular approaches have opened new windows on a host of ecological and evolutionary disciplines, ranging from population genetics and behavioral ecology to conservation biology and systematics. Molecular Markers, Natural History and Evolution summarizes the multi-faceted discoveries about organisms in nature that have stemmed from analyses of genetic markers provided by polymorphic proteins and DNAs. The first part of the book introduces rationales for the use of molecular markers, provides a history of molecular phylogenetics, and describes a wide variety of laboratory methods and interpretative tools in the field. The second and major portion of the book provides a cornucopia of biological applications for molecular markers, organized along a scale from micro-evolutionary topics (such as forensics, parentage, kinship, population structure, and intra-specific phylogeny) to macro-evolutionary themes (including species relationships and the deeper phylogenetic structure in the tree of life). Unlike most prior books in molecular evolution, the focus is on organismal natural history and evolution, with the macromolecules being the means rather than the ends of scientific inquiry. Written as an intellectual stimulus for the advanced undergraduate, graduate student, or the practicing biologist desiring a wellspring of research ideas at the interface of molecular and organismal biology, this book presents material in a manner that is both technically straightforward, yet rich with concepts and with empirical examples from the world of nature. |
| creating phylogenetic trees from dna sequences answer key: Phylogenetics E. O. Wiley, Bruce S. Lieberman, 2011-10-11 The long-awaited revision of the industry standard on phylogenetics Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of systematic biology. It has profoundly influenced the way scientists study evolution, and has seen many theoretical and technical advances as the field has continued to grow. It goes almost without saying that the next twenty-five years of phylogenetic research will prove as fascinating as the first, with many exciting developments yet to come. This new edition of Phylogenetics captures the very essence of this rapidly evolving discipline. Written for the practicing systematist and phylogeneticist, it addresses both the philosophical and technical issues of the field, as well as surveys general practices in taxonomy. Major sections of the book deal with the nature of species and higher taxa, homology and characters, trees and tree graphs, and biogeography—the purpose being to develop biologically relevant species, character, tree, and biogeographic concepts that can be applied fruitfully to phylogenetics. The book then turns its focus to phylogenetic trees, including an in-depth guide to tree-building algorithms. Additional coverage includes: Parsimony and parsimony analysis Parametric phylogenetics including maximum likelihood and Bayesian approaches Phylogenetic classification Critiques of evolutionary taxonomy, phenetics, and transformed cladistics Specimen selection, field collecting, and curating Systematic publication and the rules of nomenclature Providing a thorough synthesis of the field, this important update to Phylogenetics is essential for students and researchers in the areas of evolutionary biology, molecular evolution, genetics and evolutionary genetics, paleontology, physical anthropology, and zoology. |
| creating phylogenetic trees from dna sequences answer key: How and Why Species Multiply Peter R. Grant, B. Rosemary Grant, 2011-05-29 Trace the evolutionary history of fourteen different species of finches on the Galapagos Islands that were studied by Charles Darwin. |
| creating phylogenetic trees from dna sequences answer key: The Timetree of Life S. Blair Hedges, Sudhir Kumar, 2009-04-23 The evolutionary history of life includes two primary components: phylogeny and timescale. Phylogeny refers to the branching order (relationships) of species or other taxa within a group and is crucial for understanding the inheritance of traits and for erecting classifications. However, a timescale is equally important because it provides a way to compare phylogeny directly with the evolution of other organisms and with planetary history such as geology, climate, extraterrestrialimpacts, and other features.The Timetree of Life is the first reference book to synthesize the wealth of information relating to the temporal component of phylogenetic trees. In the past, biologists have relied exclusively upon the fossil record to infer an evolutionary timescale. However, recent revolutionary advances in molecular biology have made it possible to not only estimate the relationships of many groups of organisms, but also to estimate their times of divergence with molecular clocks. The routineestimation and utilization of these so-called 'time-trees' could add exciting new dimensions to biology including enhanced opportunities to integrate large molecular data sets with fossil and biogeographic evidence (and thereby foster greater communication between molecular and traditional systematists). Theycould help estimate not only ancestral character states but also evolutionary rates in numerous categories of organismal phenotype; establish more reliable associations between causal historical processes and biological outcomes; develop a universally standardized scheme for biological classifications; and generally promote novel avenues of thought in many arenas of comparative evolutionary biology.This authoritative reference work brings together, for the first time, experts on all major groups of organisms to assemble a timetree of life. The result is a comprehensive resource on evolutionary history which will be an indispensable reference for scientists, educators, and students in the life sciences, earth sciences, and molecular biology. For each major group of organism, a representative is illustrated and a timetree of families and higher taxonomic groups is shown. Basic aspects ofthe evolutionary history of the group, the fossil record, and competing hypotheses of relationships are discussed. Details of the divergence times are presented for each node in the timetree, and primary literature references are included. The book is complemented by an online database(www.timetree.net) which allows researchers to both deposit and retrieve data. |
| creating phylogenetic trees from dna sequences answer key: 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, 2017-03-21 The essential one-volume reference to evolution The Princeton Guide to Evolution is a comprehensive, concise, and authoritative reference to the major subjects and key concepts in evolutionary biology, from genes to mass extinctions. Edited by a distinguished team of evolutionary biologists, with contributions from leading researchers, the guide contains some 100 clear, accurate, and up-to-date articles on the most important topics in seven major areas: phylogenetics and the history of life; selection and adaptation; evolutionary processes; genes, genomes, and phenotypes; speciation and macroevolution; evolution of behavior, society, and humans; and evolution and modern society. Complete with more than 100 illustrations (including eight pages in color), glossaries of key terms, suggestions for further reading on each topic, and an index, this is an essential volume for undergraduate and graduate students, scientists in related fields, and anyone else with a serious interest in evolution. Explains key topics in some 100 concise and authoritative articles written by a team of leading evolutionary biologists Contains more than 100 illustrations, including eight pages in color Each article includes an outline, glossary, bibliography, and cross-references Covers phylogenetics and the history of life; selection and adaptation; evolutionary processes; genes, genomes, and phenotypes; speciation and macroevolution; evolution of behavior, society, and humans; and evolution and modern society |
| creating phylogenetic trees from dna sequences answer key: Phylogenetic Trees Made Easy Barry G. Hall, 2008 Barry G. Hall helps beginners get started in creating phylogenetic trees from protein or nucleic acid sequence data. |
| creating phylogenetic trees from dna sequences answer key: Principles of Population Genetics Daniel L. Hartl, Andrew G. Clark, 2007 This edition provides a balanced presentation of theory and observation. It introduces the principles of genetics and statistics that are relevant to population studies, and examines the forces affecting genetic variation from the molecular to the organismic level. |
| creating phylogenetic trees from dna sequences answer key: DNA Barcodes Ida Lopez, David L. Erickson, 2012-06-12 A DNA barcode in its simplest definition is one or more short gene sequences taken from a standardized portion of the genome that is used to identify species through reference to DNA sequence libraries or databases. In DNA Barcodes: Methods and Protocols expert researchers in the field detail many of the methods which are now commonly used with DNA barcodes. These methods include the latest information on techniques for generating, applying, and analyzing DNA barcodes across the Tree of Life including animals, fungi, protists, algae, and plants. Written in the highly successful Methods in Molecular BiologyTM series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, DNA Barcodes: Methods and Protocols aids scientists in continuing to study methods from wet-lab protocols, statistical, and ecological analyses along with guides to future, large-scale collections campaigns. |
| creating phylogenetic trees from dna sequences answer key: Bioinformatics and Molecular Evolution Paul G. Higgs, Teresa K. Attwood, 2013-04-30 In the current era of complete genome sequencing, Bioinformatics and Molecular Evolution provides an up-to-date and comprehensive introduction to bioinformatics in the context of evolutionary biology. This accessible text: provides a thorough examination of sequence analysis, biological databases, pattern recognition, and applications to genomics, microarrays, and proteomics emphasizes the theoretical and statistical methods used in bioinformatics programs in a way that is accessible to biological science students places bioinformatics in the context of evolutionary biology, including population genetics, molecular evolution, molecular phylogenetics, and their applications features end-of-chapter problems and self-tests to help students synthesize the materials and apply their understanding is accompanied by a dedicated website - www.blackwellpublishing.com/higgs - containing downloadable sequences, links to web resources, answers to self-test questions, and all artwork in downloadable format (artwork also available to instructors on CD-ROM). This important textbook will equip readers with a thorough understanding of the quantitative methods used in the analysis of molecular evolution, and will be essential reading for advanced undergraduates, graduates, and researchers in molecular biology, genetics, genomics, computational biology, and bioinformatics courses. |
| creating phylogenetic trees from dna sequences answer key: Molecular Evolutionary Genetics Masatoshi Nei, 1987 -- The Scientist |
| creating phylogenetic trees from dna sequences answer key: The Beak of the Finch Jonathan Weiner, 2014-05-14 PULITZER PRIZE WINNER • A dramatic story of groundbreaking scientific research of Darwin's discovery of evolution that spark[s] not just the intellect, but the imagination (Washington Post Book World). “Admirable and much-needed.... Weiner’s triumph is to reveal how evolution and science work, and to let them speak clearly for themselves.”—The New York Times Book Review On a desert island in the heart of the Galapagos archipelago, where Darwin received his first inklings of the theory of evolution, two scientists, Peter and Rosemary Grant, have spent twenty years proving that Darwin did not know the strength of his own theory. For among the finches of Daphne Major, natural selection is neither rare nor slow: it is taking place by the hour, and we can watch. In this remarkable story, Jonathan Weiner follows these scientists as they watch Darwin's finches and come up with a new understanding of life itself. The Beak of the Finch is an elegantly written and compelling masterpiece of theory and explication in the tradition of Stephen Jay Gould. |
| creating phylogenetic trees from dna sequences answer key: Lizards in an Evolutionary Tree Jonathan B. Losos, 2011-02-09 In a book both beautifully illustrated and deeply informative, Jonathan Losos, a leader in evolutionary ecology, celebrates and analyzes the diversity of the natural world that the fascinating anoline lizards epitomize. Readers who are drawn to nature by its beauty or its intellectual challenges—or both—will find his book rewarding.—Douglas J. Futuyma, State University of New York, Stony Brook This book is destined to become a classic. It is scholarly, informative, stimulating, and highly readable, and will inspire a generation of students.—Peter R. Grant, author of How and Why Species Multiply: The Radiation of Darwin's Finches Anoline lizards experienced a spectacular adaptive radiation in the dynamic landscape of the Caribbean islands. The radiation has extended over a long period of time and has featured separate radiations on the larger islands. Losos, the leading active student of these lizards, presents an integrated and synthetic overview, summarizing the enormous and multidimensional research literature. This engaging book makes a wonderful example of an adaptive radiation accessible to all, and the lavish illustrations, especially the photographs, make the anoles come alive in one's mind.—David Wake, University of California, Berkeley This magnificent book is a celebration and synthesis of one of the most eventful adaptive radiations known. With disarming prose and personal narrative Jonathan Losos shows how an obsession, beginning at age ten, became a methodology and a research plan that, together with studies by colleagues and predecessors, culminated in many of the principles we now regard as true about the origins and maintenance of biodiversity. This work combines rigorous analysis and glorious natural history in a unique volume that stands with books by the Grants on Darwin's finches among the most informed and engaging accounts ever written on the evolution of a group of organisms in nature.—Dolph Schluter, author of The Ecology of Adaptive Radiation |
| creating phylogenetic trees from dna sequences answer key: Phylogenetic Analysis of DNA Sequences Michael M. Miyamoto, Joel Cracraft, 1991-11-14 With increasing frequency, systematic and evolutionary biologists have turned to the techniques of molecular biology to complement their traditional morphological and anatomical approaches to questions of the historical relationship and descent among groups of animals and plants. In particular, the comparative analysis of DNA sequences is becoming a common and important focus of research attention today. The objective of this volume is to survey the emerging field of molecular systematics of DNA sequences, and to appraise the strengths and limitations of the different approaches yielded by these techniques. The contributors are an internationally recognized group of investigators from different schools and disciplines who critically address a diversity of crucial questions about DNA systematics, including DNA sequence data acquisition, phylogenetic inference, congruence and consensus problems, limitations of molecular data, and the integration of molecular and morphological data sets. The work will interest all botanists and zoologists involved in systematics, taxonomy, and evolution. |
| creating phylogenetic trees from dna sequences answer key: Computational Phylogenetics Tandy Warnow, 2018 This book presents the foundations of phylogeny estimation and technical material enabling researchers to develop improved computational methods. |
| creating phylogenetic trees from dna sequences answer key: Bayesian Evolutionary Analysis with BEAST Alexei J. Drummond, Remco R. Bouckaert, 2015-08-06 Covers theory, practice and programming in Bayesian phylogenetics with BEAST. The why, how and what of BEAST 2. |
| creating phylogenetic trees from dna sequences answer key: The Nature of Diversity Daniel R. Brooks, Deborah A. McLennan, 2002-05-01 All living things on earth—from individual species to entire ecosystems—have evolved through time, and evolution is the acknowledged framework of modern biology. Yet many areas of biology have moved from a focus on evolution to much narrower perspectives. Daniel R. Brooks and Deborah A. McLennan argue that it is impossible to comprehend the nature of life on earth unless evolution—the history of organisms—is restored to a central position in research. They demonstrate how the phylogenetic approach can be integrated with ecological and behavioral studies to produce a richer and more complete picture of evolution. Clearly setting out the conceptual, methodological, and empirical foundations of their research program, Brooks and McLennan show how scientists can use it to unravel the evolutionary history of virtually any characteristic of any living thing, from behaviors to ecosystems. They illustrate and test their approach with examples drawn from a wide variety of species and habitats. The Nature of Diversity provides a powerful new tool for understanding, documenting, and preserving the world's biodiversity. It is an essential book for biologists working in evolution, ecology, behavior, conservation, and systematics. The argument in The Nature of Diversity greatly expands upon and refines the arguments made in the authors' previous book Phylogeny, Ecology, and Behavior. |
| creating phylogenetic trees from dna sequences answer key: Introduction to Computational Genomics Nello Cristianini, Matthew W. Hahn, 2006-12-14 Where did SARS come from? Have we inherited genes from Neanderthals? How do plants use their internal clock? The genomic revolution in biology enables us to answer such questions. But the revolution would have been impossible without the support of powerful computational and statistical methods that enable us to exploit genomic data. Many universities are introducing courses to train the next generation of bioinformaticians: biologists fluent in mathematics and computer science, and data analysts familiar with biology. This readable and entertaining book, based on successful taught courses, provides a roadmap to navigate entry to this field. It guides the reader through key achievements of bioinformatics, using a hands-on approach. Statistical sequence analysis, sequence alignment, hidden Markov models, gene and motif finding and more, are introduced in a rigorous yet accessible way. A companion website provides the reader with Matlab-related software tools for reproducing the steps demonstrated in the book. |
| creating phylogenetic trees from dna sequences answer key: Phylogenetic Trees Made Easy Barry G. Hall, 2004 |
| creating phylogenetic trees from dna sequences answer key: The Phylogenetic Handbook Marco Salemi, Anne-Mieke Vandamme, Philippe Lemey, 2009-03-26 A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools. |
| creating phylogenetic trees from dna sequences answer key: Preparing for the Biology AP Exam Neil A. Campbell, Jane B. Reece, Fred W. Holtzclaw, Theresa Knapp Holtzclaw, 2009-11-03 Fred and Theresa Holtzclaw bring over 40 years of AP Biology teaching experience to this student manual. Drawing on their rich experience as readers and faculty consultants to the College Board and their participation on the AP Test Development Committee, the Holtzclaws have designed their resource to help your students prepare for the AP Exam. Completely revised to match the new 8th edition of Biology by Campbell and Reece. New Must Know sections in each chapter focus student attention on major concepts. Study tips, information organization ideas and misconception warnings are interwoven throughout. New section reviewing the 12 required AP labs. Sample practice exams. The secret to success on the AP Biology exam is to understand what you must know and these experienced AP teachers will guide your students toward top scores! |
| creating phylogenetic trees from dna sequences answer key: Science Needs for Microbial Forensics National Research Council (U.S.). Committee on Science Needs for Microbial Forensics: Developing an Initial International Roadmap, 2014 For these reasons, building awareness of and capacity in microbial forensics can assist in our understanding of what may have occurred during a biothreat event, and international collaborations that engage the broader scientific and policy-making communities are likely to strengthen our microbial forensics capabilities. One goal would be to create a shared technical understanding of the possibilities--and limitations--of the scientific bases for microbial forensics analysis. Science Needs for Microbial Forensics: Developing Initial International Research Priorities, based partly on a workshop held in Zabgreb, Croatia in 2013, identifies scientific needs that must be addressed to improve the capabilities of microbial forensics to investigate infectious disease outbreaks and provide evidence of sufficient quality to support legal proceedings and the development of government policies. |
| creating phylogenetic trees from dna sequences answer key: Opportunities in Biology National Research Council, Division on Earth and Life Studies, Commission on Life Sciences, Board on Biology, Committee on Research Opportunities in Biology, 1989-01-01 Biology has entered an era in which interdisciplinary cooperation is at an all-time high, practical applications follow basic discoveries more quickly than ever before, and new technologiesâ€recombinant DNA, scanning tunneling microscopes, and moreâ€are revolutionizing the way science is conducted. The potential for scientific breakthroughs with significant implications for society has never been greater. Opportunities in Biology reports on the state of the new biology, taking a detailed look at the disciplines of biology; examining the advances made in medicine, agriculture, and other fields; and pointing out promising research opportunities. Authored by an expert panel representing a variety of viewpoints, this volume also offers recommendations on how to meet the infrastructure needsâ€for funding, effective information systems, and other supportâ€of future biology research. Exploring what has been accomplished and what is on the horizon, Opportunities in Biology is an indispensable resource for students, teachers, and researchers in all subdisciplines of biology as well as for research administrators and those in funding agencies. |
| creating phylogenetic trees from dna sequences answer key: Phylogenetic Systematics Willi Hennig, 1999 Phylogenetic Systematics, first published in 1966, marks a turning point in the history of systematic biology. Willi Hennig's influential synthetic work, arguing for the primacy of the phylogenetic system as the general reference system in biology, generated significant controversy and opened possibilities for evolutionary biology that are still being explored. |
| creating phylogenetic trees from dna sequences answer key: Intended Evolution Dongxun Zhang, Bob Zhang, 2015-05-05 Discover a new outlook on the process of life—and improve your health as a result In Intended Evolution, authors Dongxun and Bob Zhang introduce a different perspective on the theory of evolution: Life is not only selected by nature but intentionally interacts with it, learning how to better its future. They explain that applying this idea to generally accepted principles of biology can have startling results in your ability to affect your own health—and even your evolution. According to the theory of intended evolution, organisms gather information through sensory experience and use that knowledge to effect change in themselves and their environments. The authors propose that organisms use this saved information to make choices projected to enhance their survival. It is through experience, choices, and action, within a given environment, that life changes itself from moment to moment and determines what changes are needed for future generations. Because of humans’ unique ability to understand how our own evolution functions, we can effect changes within ourselves to influence and enhance our health and fitness, even to lengthen our lifespan. |
| creating phylogenetic trees from dna sequences answer key: Insect Phylogeny Willi Hennig, 1981 Methodological introduction; Localities for palaeozoic and mesozoic insects; The phyloggenetic development of the insecta; Concluding remarks and prospects for the future. |
| creating phylogenetic trees from dna sequences answer key: Molecular Zoology Joan D. Ferraris, Stephen R. Palumbi, 1996-05-31 Molecular Zoology Advances, Strategies, and Protocols Edited by Joan D. Ferraris and Stephen R. Palumbi Contemporary tools of molecular biology continue to open new areas of biological research and to provide important answers to classic problems. Zoological questions of mating strategies, physiological adaptation, genetic exchange between populations, cell lineages during development, and many others are now being powerfully addressed using tools from the molecular arsenal. To provide broad access to these tools requires an authoritative reference that highlights recent advances, lays out future strategies, and provides working protocols to a wide audience of zoological scientists. Molecular Zoology: Advances, Strategies, and Protocols outlines the core concepts of these critical molecular techniques and provides specific instructions for their use. The book is divided into two main parts: Research Strategies and Protocols. The first section features detailed descriptions of the research approaches that incorporate molecular tools in the study of developmental, physiological, ecological, and evolutionary processes. In addition to charting recent advances, this section shows how to interpret results and describes the advantages and disadvantages of alternative approaches. These chapters function as entry points to molecular zoology for broadly trained zoologists without formal molecular training, graduate students, and molecular biologists in other fields. The second section is a compilation of over 60 protocols which have been developed, tested, and perfected by leading researchers in the field. It provides step-by-step coverage of each protocol, featuring for each a summary of its underlying rationale, a list of necessary reagents and solutions, and a discussion of potential obstacles to a particular technique. Specific techniques covered in the book include: * Applications of parametric bootstrapping in molecular phylogenetics * Microsatellite analysis of genetic mating systems and genetic relatedness * Use of RAPD-PCR markers in genetic structure and genealogies * PCR-based cloning across large taxonomic distances * Cell lineage analysis using retroviral vectors * Osmoregulatory gene characterization and expression * Regulatory element identification and transcription factor analysis * Protocols for in situ hybridization, DNA footprinting, gene knockout, ribonuclease protection assay, and coupled transcription/translation reactions. Molecular Zoology: Advances, Strategies, and Protocols is an authoritative resource designed to provide both basic and in-depth explanations of molecular investigation procedures for research scientists in all areas of organismal and integrative biology, including zoology, marine biology, and ecology. With its extensive coverage of molecular protocols, graduate students in biology will also find this book to be an indispensable manual for laboratory work. |
| creating phylogenetic trees from dna sequences answer key: The New Science of Metagenomics National Research Council, Division on Earth and Life Studies, Board on Life Sciences, Committee on Metagenomics: Challenges and Functional Applications, 2007-06-24 Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a meta view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a Global Metagenomics Initiative comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field. |
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