Experimental Phylogenetics
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Digital Evolution In Experimental Phylogenetics And Evolution Education
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Author : Cory Kohn
language : en
Publisher:
Release Date : 2021
Digital Evolution In Experimental Phylogenetics And Evolution Education written by Cory Kohn and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with Electronic dissertations categories.
The creation and evaluation of known evolutionary histories and the implementation of student investigatory experiences on evolution are difficult endeavors that have only recently been feasible. The research presented in this dissertation is related in their shared use of digital evolution with Avidians as a model study system, both to conduct science research in experimental phylogenetics and to conduct education research in curricular intervention to aid student understanding.I first present background discussions on the Avidian digital evolution study system—as implemented in Avida and Avida-ED—and its favorable use in experimental phylogenetics and biology education owing to its greater biological realism than computational simulations, and greater utility and generality than biological systems. Prior work on conducting experimental evolution for use in phylogenetics and work on developing undergraduate lab curricula using experimental evolution are also reviewed.I establish digital evolution as an effective method for phylogenetic inference validation by demonstrating that results from a known Avidian evolutionary history are concordant, under similar conditions, to established biological experimental phylogenetics work. I then further demonstrate the greater utility and generality of digital evolution over biological systems by experimentally testing how phylogenetic accuracy may be reduced by complex evolutionary processes operating singly or in combination, including absolute and relative degrees of evolutionary change between lineages (i.e., inferred branch lengths), recombination, and natural selection. These results include that directional selection aids phylogenetic inference, while stabilizing selection impedes it. By evaluating clade accuracy and clade resolvability across treatments, I evaluate measures of tree support and its presentation in the form of consensus topologies and I offer several general recommendations for systematists.Using a larger and more biologically realistic experimental design, I systematically examine a few of the complex processes that are hypothesized to affect phylogenetic accuracy—natural selection, recombination, and deviations from the model of evolution. By analyzing the substitutions that occurred and calculating selection coefficients for derived alleles throughout their evolutionary trajectories to fixation, I show that molecular evolution in these experiments is complex and proceeding largely as would be expected for biological populations. Using these data to construct empirical substitution models, I demonstrate that phylogenetic inference is incredibly robust to significant molecular evolution model deviations. I show that neutral evolution in the presence of always-occurring population processes, such as clonal or Hill-Robertson interference and lineage sorting, result in reduced clade support, and that selection and especially recombination, including their joint occurrence, restore this otherwise-reduced phylogenetic accuracy. Finally, this work demonstrates that inferred branch lengths are often quite inaccurate despite clade support being accurate. While phylogenetic inference methods performed relatively well in both theoretically facile and challenging molecular evolution scenarios, their accuracy in clade support might be a remarkable case of being right for misguided reasons, since branch length inference were largely inaccurate, and drastically different models of evolution made little difference. This work highlights the need for further research that evaluates phylogenetic methods under experimental conditions and suggests that digital evolution has a role here.Finally, I examine student understanding of the importance of biological variation in the context of a course featuring a digital evolution lab. I first describe the Avida-ED lab curriculum and its fulfillment of calls for reform in education. Then I describe the specific education context and other course features that aim to address student conceptualization of variation. I present a modified published assessment on transformational and variational understanding and findings regarding student understanding of variation within an evolution education progression. Finally, I offer suggestions on incorporating course material to engage student understanding of variation.
Experimental Phylogenetics
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Author : Ryan Nicole Randall
language : en
Publisher:
Release Date : 2012
Experimental Phylogenetics written by Ryan Nicole Randall and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012 with Evolution (Biology) categories.
The field of molecular evolution has benefited greatly from the use of ancestral sequence reconstruction as a methodology to better understand the molecular mechanisms associated with functional divergence. The method of ancestral sequence reconstruction has never been experimentally validated despite the method being exploited to generate high profile publications and gaining wider use in many laboratories. The failure to validate such a method is a consequence of 1) our inability to travel back in time to document evolutionary transitions and 2) the slow pace of natural evolutionary processes that prevent biologists from 'witnessing' evolution in action (pace viruses). In this thesis research, we have generated an experimentally known phylogeny of fluorescent proteins in order to benchmark ancestral sequence reconstruction methods. The tips/leaves of the fluorescent protein experimental phylogeny are used to determine the performances of various ASR methods. This is the first example of combining experimental phylogenetics and ancestral sequence reconstruction.
Experimental Evolution
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Author : Theodore Garland
language : en
Publisher: Univ of California Press
Release Date : 2009-12-03
Experimental Evolution written by Theodore Garland and has been published by Univ of California Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-12-03 with Science categories.
Experimental approaches to evolution provide indisputable evidence of evolution by directly observing the process at work. Experimental evolution deliberately duplicates evolutionary processes—forcing life histories to evolve, producing adaptations to stressful environmental conditions, and generating lineage splitting to create incipient species. This unique volume summarizes studies in experimental evolution, outlining current techniques and applications, and presenting the field’s full range of research—from selection in the laboratory to the manipulation of populations in the wild. It provides work on such key biological problems as the evolution of Darwinian fitness, sexual reproduction, life history, athletic performance, and learning.
Text Mining Of Experimental Methods In Phylogenetics
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Author : James Matthew Eales
language : en
Publisher:
Release Date : 2010
Text Mining Of Experimental Methods In Phylogenetics written by James Matthew Eales and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with categories.
Text Mining Of Experimental Methods In Phylogenetics
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Author : James Matthew Eales
language : en
Publisher:
Release Date : 2010
Text Mining Of Experimental Methods In Phylogenetics written by James Matthew Eales and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010 with categories.
Experimental Design And The Detection Of Adaptive Molecular Divergence In Phylogenetics And Genomics
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Author : A. P. Jason De Koning
language : en
Publisher:
Release Date : 2007
Experimental Design And The Detection Of Adaptive Molecular Divergence In Phylogenetics And Genomics written by A. P. Jason De Koning and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007 with Divergence (Biology) categories.
Phylogenetics A Hands On Introduction
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Author : Stilianos Louca
language : en
Publisher: Stilianos Louca
Release Date : 2023-06-07
Phylogenetics A Hands On Introduction written by Stilianos Louca and has been published by Stilianos Louca this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-06-07 with Science categories.
This book introduces concepts of modern phylogenetics through hands-on examples, including how to construct, read and analyze phylogenetic trees in the command line and in R. The book targets undergraduate and graduate students in biology, bioinformatics, data science or related fields. Numerous examples and exercises are included throughout the book, mostly using data from the scientific literature. Phylogenies used in the examples/exercises span the entire tree of life including viruses, bacteria, archaea and eukaryotes. Prerequisites include basic familiarity with the command line (bash) and with R. References to the scientific literature are provided throughout for the interested reader. This book is suitable as reading material in related university courses as well as for self-teaching.
The Evolution Of Phylogenetic Systematics
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Author : Andrew Hamilton
language : en
Publisher: Univ of California Press
Release Date : 2013-11-09
The Evolution Of Phylogenetic Systematics written by Andrew Hamilton and has been published by Univ of California Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-11-09 with Science categories.
The Evolution of Phylogenetic Systematics aims to make sense of the rise of phylogenetic systematicsÑits methods, its objects of study, and its theoretical foundationsÑwith contributions from historians, philosophers, and biologists. This volume articulates an intellectual agenda for the study of systematics and taxonomy in a way that connects classification with larger historical themes in the biological sciences, including morphology, experimental and observational approaches, evolution, biogeography, debates over form and function, character transformation, development, and biodiversity. It aims to provide frameworks for answering the question: how did systematics become phylogenetic?
The Tree With Many Branches
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Author : Tommy Rodriguez
language : en
Publisher: iUniverse
Release Date : 2020-08-20
The Tree With Many Branches written by Tommy Rodriguez and has been published by iUniverse this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-08-20 with Science categories.
Want to build an evolutionary tree? Here’s your chance to learn how. The field of bioinformatics was born out of the need to manage, analyze, and examine raw genomic data in meaningful and exciting ways, such as the discipline of computational phylogenetics would provide. The evolutionary inferences reached among the several peer-reviewed articles contained in this book are neither novel nor breakthrough. However, it is in the application of computational techniques, experiment design, and probabilistic models where this research finds a stronghold. As a matter of practicality, the original manuscripts have been edited for a broader audience due to its highly technical language. The essays compiled in these pages have undergone a facelift, from their original scientific format into a more reader-friendly layout, as to better accommodate two different perspectives – both experts and non-experts alike.
Phylogenetics
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Author : E. O. Wiley
language : en
Publisher: John Wiley & Sons
Release Date : 2011-06-07
Phylogenetics written by E. O. Wiley and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2011-06-07 with Science categories.
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.
