15 Best Phylogenetics Books To Read in [2022] [UPDATED]

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Science and Biology would not be so captivating if there were no bones of dinosaurs left around. We dug the earth and found marvels.

Computers and technologies helped to predict the structure and phenotype of ancestral organisms accurately. And years later we saw movies. It doesn’t come as a surprise too when we compare humans to Apes and Chimpanzees.

Evolutionary studies and Phylogenetics are as fascinating as they sound. Here is a list of the Best textbooks on Phylogenetics that would enhance your interest in the subject. This list is a complete package for all kinds of studies possible on Phylogenetics.


Best Phylogenetics Books To Be Read By Molecular and Evolutionary Biologists For Research

Out of these many influential books, I would recommend you the following ones to read from.


1. Tree Thinking: An Introduction to Phylogenetic Biology

Tree thinking: An Introduction to Phylogenetic Biology is written by David A Baum and Stacey D Smith. Both the writers are expert evolutionary biology researchers and professors in the field of systematics.

In this volume, they have described a brief introduction to Phylogenetics and its significance in present-day biology.

Darwin, the Pioneer of evolution and science, had displayed the branching trees or phylogenies in the organisms he had studied during his research.

Genetics is an undermine field of biology. However, the recent developments in the subject are appreciated. It has broad applications in biology, from discovering the characteristics in ancient organisms to finding the source of invasive species and infectious diseases to knowing the closest living relative and extinct species.

Why You Should Buy This Book

  • The book is a basic outline of a treasured subject of Phylogenetic.
  • It adopts a conceptual approach to clear the relevant themes.
  • The interpretation of phylogenetic trees, their construction, and answering the biological questions have been taken care of.
  • Each chapter concludes with a set of mind-boggling questions that would clear the concepts of the reader.
  • The book could be a critical tool in practically training the future evolutionary biologist

Level (best suitable for): Beginner to Intermediate


2. On the Origin of Phyla

On the Origin of Phyla, authored by James Valentine, sounds similar to the remarkable book- On the Origin of Species by Darwin, since James Valentine drew inspiration from this extraordinary book. Valentine has thoroughly studied Darwin’s research collection and his books and tried to find answers On the Origin of Phyla.

Valentine is one of the most distinguished paleobiologists.

He has integrated the data from evolutionary biology, embryology, comparative morphology, molecular genetics, developmental biology, and palaeontology to interest the experts from any of these fields.

He has carefully examined the shreds of evidence, such as fossils, morphology, and molecules. He has compared the fundamental morphology and the development of the animal kingdom.

He has laid particular emphasis on the valuable design elements found in the body structure of both living and extinct species.

Some of the cherished chapters include the explanatory way of developing modes to explain the origin and diversification in the animal kingdom and their evolutionary patterns.

Why You Should Buy This Book

  • One of the classic scientific textbooks for Phylogenetics that affects the work in the fields of developmental, molecular, and evolutionary sciences.
  • Intelligent and logical evaluation of the pieces of evidence of evolution
  • Integrated data from different domains of science and hence can be beneficial to distinctive research groups

Level (best suitable for): Beginner to Intermediate


3. The Tangled Tree: A Radical New History of Life

The Tangled Tree: A Radical New History of Life is written by well-known writer David Quammen. The book is not just another Phylogenetics book but, it is a unique collection on how recent discoveries in molecular biology have affected our understanding of evolution and the history of life.

David has made the concept of molecular biology and evolution easy-to-understand via his persuasive writing skills.

He has included information on Carl Woese, Lynn Margulis, Tsutomu Watanabe, and many more who have contributed to the field of evolutionary sciences.

The author has explained about the tangled tree of life through molecular studies. He has included the fact about the position of humans in that tree.

Why You Should Buy This Book

  • Storybook like flow to make it interesting for the readers
  • Simple and easy language makes it worth reading.
  • A well-informed guide to explain the complicated history and story of evolution
  • David has written an innovative and creative text for his intellectual adventurers.

Level (best suitable for): Intermediate to Advance


4. Inferring Phylogenies

Inferring Phylogenies written by Joseph Felsenstein is a fundamental and in-depth analysis volume on evolutionary trees and comparative analysis between different species.

For more than 40 years, the development in computational, statistical, and algorithmic work is going on. Inferring phylogenies has summarized the work done until now in an explanatory and brief way.

The book draws a logical explanation about the phylogenies and their inferences.

The book is divided into 30 chapters almost. The starting chapter begins with the fundamental issues of counting the evolutionary changes. It goes on to cover the inference algorithms, distance methods, likelihood methods, and their implementations.

The latter chapters of the book include statistical analysis of phylogenies, tree comparison, evaluation of statistical support for tree topologies, and so on.

Why You Should Buy This Book

  • A must-read book for any learner who wants to understand how phylogenies are reconstructed and how to analyze the inferences
  • The book focuses on the data searches, discreetly coded characters, molecular sequences, quantitative characters, and gene frequencies
  • It includes restriction sites, RAPDs, and microsatellites.
  • The book is written for graduate-level students provided they have previous knowledge of mathematics, molecular sequences, statistics, and quantitative genetics

Level (best suitable for): Beginner to Intermediate


5. The Phylogenetic Handbook

The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing provides a comprehensive beginning to the theory and practice of phylogenetic analysis.

The book includes 8 sections and 21 chapters in total. The book begins with the basic concepts of molecular evolution. Chapters, later on, include sequence databases and searching in those databases, and the multiple sequence alignment.

The most notable section is the third section that includes methods of phylogenetic inferences. Section four includes the models and trees for evolutionary studies.

The later chapters include the recombination detection and characterization of individual recombination events.

Population genetics and additional topics such as substitution saturation and split networks have been discussed at the end of the book.

Why You Should Buy This Book

  • The book focuses on hypothesis testing and extensive discussion on recombination analysis, detecting molecular adaptation, and population genetics
  • The book is a practical approach to test and verify the hypothesis
  • A brief description of phylogenetic software such as BLAST, Clustal, T-coffee, Muscle, BEAST, LAMARC, IQPNNI, CONSEL, Model test, PAML, HYPHY, MEGA.
  • Written by the original authors who explain their tools in a descriptive way
  • An ideal guide for undergraduate and graduate students

Level (best suitable for): Intermediate to Advance


6. Molecular Evolution and Phylogenetics

Molecular Evolution and Phylogenetics is written by Sudhir Kumar from the Arizona State University and Masatoshi Nei from Pennsylvania State University.

The book is divided into several sections. The first section is a clear and detailed description of nucleic acid sequence comparisons.

The book is mostly about Phylogenetics and mathematics for describing the analysis approaches. The appropriate math and formulas are present for the real understanding of the subject.

The last section is about population genetics. This topic has been found in most of the phylogenetic books, and hence it is significant to find this topic here as well. Population genetics is the background model behind the functions that calculate, score the differences in population.

Overall, the textbook includes topics of sequence divergence, phylogenetic tree construction, a statistical test for detection of Darwinian selection, construction of linearized trees, and inference of ancestral amino acid sequence analysis of allele frequency data.

Practical methods of data analysis using computer software such as MEGA2 has been focused on.

Why You Should Buy This Book

  • The chapters are clear cut, and the examples have been given to make things understandable
  • A good book for beginners learning about molecular evolutionary analysis.
  • Straight forward writing with easy words for understanding
  • Overall a complete guide for molecular evolution and basic DNA analysis techniques
  • Recommended for scientists with the mathematical and statistical background

Level (best suitable for): Beginner to Intermediate


7. Phylogenetics: Theory and Practice of Phylogenetic Systematics

Phylogenetics: Theory and Practice of Phylogenetic Systematics authored by E.O. Wiley and Bruce S. Lieberman is a classic volume in the phylogenetic genre of science. The book has been highly acclaimed for its achievements in systematic biology.

The book is written for researchers working in the field of systems biology and evolutionary Phylogenetics.

The book addresses the technical and philosophical aspects of the field. It includes surveys and general practices in taxonomy.

The book majorly deals in the species of higher taxa, their homology, and characters. Sections include the construction of tree graphs and biogeography concepts that can be applied Phylogenetics.

The additional sections include the deep guide for tree building algorithms. This includes phylogenetic classification, specimen selection, field collecting, curating, automatic publication, and the rules of nomenclature, parametric Phylogenetics like maximum likelihood and Bayesian approaches, parsimony and parsimony analysis, evolutionary taxonomy, genetics, and transformed cladistics

Why You Should Buy This Book

  • A remarkable book for researchers in the field of molecular evolution, genetics, evolutionary biology, evolutionary genetics, zoology, bioinformatics, paleontology, etc
  • It includes the updated information on new computational methods
  • Relevant and useful examples at appropriate places

Level (best suitable for): Intermediate to Advance


8. Molecular Evolution: A Statistical Approach

Molecular evolution: A Statistical Approach is written by Ziheng Yang, a professor of statistical genetics at University College London.

Professor Yang has represented the modern statistical methods and computational algorithms for the comparative analysis of sequence and genetic data in the fields of molecular evolution, Phylogenetics, statistical phylogeography, comparative and structural genomics.

The author has comprehensively written about the maximum likelihood and Bayesian methods for studies.

The expertise knowledge of the author has led to the accomplishment of the book with the conceptual understanding of the topics rather than a mathematical approach.

Why You Should Buy This Book

  • The text is filled with real-life data and calculations to verify the theories. Suitable examples that work on the problems are present at the end of each chapter.
  • It is an advanced book for graduate-level students and researchers.
  • The book is liked and appreciated by researchers across the globe and has received positive reviews on the writing style.
  • Appropriate for computational biology, statistical genomics, molecular systematics, evolutionary biology, evolutionary genetics, mathematics, statistics, and so on

Level (best suitable for): Advanced


9. Bayesian Phylogenetics

Bayesian Phylogenetic: Methods, Algorithms, and Applications edited by a group of 3 renowned editors are a compilation of the rich diversity of phylogenetic models.

The book includes details on Bayesian phylogenetic which would allow the evolutionary biologists, ecologists, epidemiologists, and systematists to find answers to bizarre phylogenetic questions.

The core theme of the book is Bayesian methods and current trends in research.

The book includes up-to-date interdisciplinary research on the Bayesian statistical model. It focuses on model selection, recent researches of interest, and development.

It also includes mixing up new methods in Bayesian analysis through which tree topology changes.

The book is detailed coverage of the divergence of time estimation, realistic models, and the burgeoning interface of Phylogenetics and population genetics.

Why You Should Buy This Book

  • Concrete knowledge about the Bayesian method for genetics and its sub-areas of research. A guide and roadmap to the researcher starting to working on this field.
  • Concise book with typical examples for every topic along with clear and relevant illustrations.
  • The book is suitable for graduate-level researchers in mathematics, statistics, and evolutionary biology

Level (best suitable for): Intermediate to Advance


10. Phylogenetic Trees Made Easy: A How-To Manual

Phylogenetic trees made easy: A How-to Manual authored by Berry G Hall is a practical guide for solving the scientific problems based on genetic analysis and protein and nucleic acid sequence data.

The book is written keeping the theoretical phylogeneticists in mind however it can also serve the scientific researchers at the molecular level to the cellular biologists who may or may not be familiar with the evolutionary basis of Phylogenetics study.

Why You Should Buy This Book

  • The reader is guided step by step to understand the protocol of phylogenetic analysis
  • An understanding of identifying the relevant sequences that should be included in a tree becomes clear
  • The aligning of sequences, estimating the tree development by one or the other several methods, and drawing a tree with high relevance can be learned
  • Special boxes labeled “learn more” is mentioned throughout the book that includes the various concepts and background information.
  • The protocols are written in clear, easy, and understandable language
  • Students at the graduate and postgraduate level can read the book for a clear understanding of evolutionary science
  • Highly recommended for those who build concepts by the practical approach

Level (best suitable for): Intermediate to Advance


11. Computational Phylogenetics

Computational Phylogenetics: an introduction to designing methods for phylogeny estimation written by Tandy Warnow is an amazing collection of the basic and advanced material for phylogeny estimation and analysis.

The core idea of the book is to lay special focus on computational and statistical methods for advanced phylogenetic learning.

The book is interdisciplinary, which means students from any background belonging to biology computer science, statistics mathematics, and so on will find the book very helpful.

The book is a detailed description of the statistical and mathematical approach for solving the phylogenetic estimation and also represents the advanced material for such studies.

The author has brilliantly developed analytical techniques to validate the theoretical properties of the methods. He has also addressed performance in practice for the different methods of estimating phylogenetic trees.

Why You Should Buy This Book

  • Students belonging to the field of computational Phylogenetics would find this book is a true guide for acquiring knowledge on novel computational methods.
  • The text is comprehensive and includes both basic and advanced material
  • Interdisciplinary science book and hence recommended for researches from varying disciplines.

Level (best suitable for): Intermediate to Advance


12. Plant Systematics: A Phylogenetic Approach

Plant systematics: A phylogenetic approach is written by a group of 5 esteemed writers. It is a compilation of vascular plant phylogeny written by experts in their fields.

Plants and general flora has been studied for years. They were the earliest life forms on earth and hence their phylogenetic study is significantly important.

With the development of plant systematics in recent years, the need for phylogenetic analysis has also increased.

This book is a great compilation of similar plant systematics phylogenetic studies. The text is divided into various chapters and each includes separate and relevant topics.

The introduction is comprehensive and clear. The text provides a description of several plant families to represent monophyletic groups. It also exemplifies the classification of the angiosperm phylogeny group.

Why You Should Buy This Book

  • Text is written in simple, clear, and understandable language.
  • It includes informative drawings to support the text.
  • The appendices include botanical nomenclature and herbarium methodology. The book is devoted to the systematics of angiosperms, vascular plants, and local flora. The book includes basic topics, hence readers will find it easy and fundamental
  • The pictures are of high quality and beautiful
  • The book is engaging due to the nice flow of text and easy transformation from one chapter to another.

Level (best suitable for): Beginner to Intermediate


13. Mathematics of Evolution and Phylogeny

Mathematics of Evolution and Phylogeny edited by Olivier Gascuel is comprehensive and in-depth mathematics on phylogenetic studies.

It includes the computational and algorithmic aspects of understanding evolution.

The book provides an insight into the famous and successful work on phylogenies by a computational biologist, mathematician, and statistician.

The book considers evolution not merely as a biological and historical phenomenon limited to genes, sequences, genomes, and species but more than that.

Why You Should Buy This Book

  • It focuses on the computational tools and mathematical formulas that can form the basis of evolutionary studies.
  • These studies can help to identify the limitations of the previous methodologies. It can provide the progress and future that mathematics could offer to this complex and realistic science field.
  • Recommended for core mathematicians, a computational biologist, and evolutionary study scientists
  • An advanced book with great potential of contribution in solving evolutionary problems

Level (best suitable for): Intermediate to Advance

Also Check:

14. Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology

Modern fellow genetic comparative methods and their application in evolutionary biology: Concepts and Practice provide an overview of newly developed advanced phylogenetic and comparative tools that can allow investigation on a broad range of questions.

The complex questions like how phenotypic characters develop along the branches of phylogeny and how such changes add to the complex shape of animal communities and interspecific interactions can be answered by this book.

The chapters are written by individuals who are experts in the field. The authors briefly explain the different methodologies that provide pieces of evidence on the implementation of the methods in real life.

Why You Should Buy This Book

  • The book is a valuable resource for conceptual and practical materials for expanding the knowledge of both educators and learners
  • The book comes along with online resources where the authors update the practical material as well as theoretical material.
  • Since phylogenetic comparative studies have become a powerful tool for analysis to make inferences from evolutionary data of interspecific organisms and phylogenies, this book is recommended for every learner of evolutionary science.
  • The evolutionary tool kit is rapidly increasing in quality and quantity, and these methodological papers published in the book can help scientists to solve incomprehensible problems.

Level (best suitable for): Intermediate to Advance


15. Analysis of Phylogenetics and Evolution with R

Analysis of Phylogenetics and evolution with R (Use R!) is written by famous Emmanuel Paradis.

Every day the database for molecular and genetic studies is increasing at a great pace. With the increase in computational capacity, the probability of assessing and reassessing the data for molecular evolution patterns, and the role in adaptation in species diversity can be studied.

The book is a compilation of a wide variety of methods on data analysis into a single platform that is the R language. It is an open-source language and is available globally on any computer system.

The book has been divided into various sections where the initial chapters include a basic introduction of R packages.

The basic phylogenetic topics such as manipulation of data, drawing of a phylogenetic tree, comparative study methods, estimation, etc. have been included.

It further includes topics on genetic tree drawing using R as a powerful graphical interface. The analysis of diversification is included towards the end.

The last chapter includes the development of methods in phylogeny with R with other languages like C and C++.

Why You Should Buy This Book

  • Adopting R language as a tool for phylogenetic analysis will reduce the hurdles of biologists in data analysis
  • It also ensures great scientific reliability and exchange of ideas and development of methods.
  • A great guidebook for graduates and researchers in evolutionary science and computational biology.
  • This makes the process of data analysis easy to understand
  • The chapters are brief and include a significant chapter on simulation of evolutionary data.
  • It has been adopted by many scientists for statistical analysis.
  • Bioinformaticians can learn the implementation of these methods in the R language

Level (best suitable for): Advanced

These are the best 15 textbooks for Phylogenetics study.

These books are an amalgamation of all kinds of topics under a single theme of Phylogenetics. It includes practical guides and laboratory manuals, theoretical concepts with illustrations, and advanced computational algorithms, and mathematical approaches.

Pick anyone out of them for a brief introduction to the basics of Evolutionary sciences. Reading specific books would guide you to select the methodologies for your research and experiments appropriately.

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