Testing Character Evolution Models In Phylogenetic Paleobiology
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Author | : April Wright |
Publisher | : Cambridge University Press |
Total Pages | : 80 |
Release | : 2021-08-26 |
Genre | : Science |
ISBN | : 100905872X |
Macroevolutionary inference has historically been treated as a two-step process, involving the inference of a tree, and then inference of a macroevolutionary model using that tree. Newer models blend the two steps. These methods make more complete use of fossils than the previous generation of Bayesian phylogenetic models. They also involve many more parameters than prior models, including parameters about which empiricists may have little intuition. In this Element, we set forth a framework for fitting complex, hierarchical models. The authors ultimately fit and use a joint tree and diversification model to estimate a dated phylogeny of the Cincta (Echinodermata), a morphologically distinct group of Cambrian echinoderms that lack the fivefold radial symmetry characteristic of extant members of the phylum. Although the phylogeny of cinctans remains poorly supported in places, this Element shows how models of character change and diversification contribute to understanding patterns of phylogenetic relatedness and testing macroevolutionary hypotheses.
Author | : Emmanuel Paradis |
Publisher | : Springer Science & Business Media |
Total Pages | : 221 |
Release | : 2006-11-25 |
Genre | : Science |
ISBN | : 0387351000 |
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.
Author | : Eric J. Sargis |
Publisher | : Springer Science & Business Media |
Total Pages | : 453 |
Release | : 2008-05-21 |
Genre | : Science |
ISBN | : 1402069979 |
This book celebrates the contributions of Dr. Frederick S. Szalay to the field of Mammalian Evolutionary Morphology. Professor Szalay is a strong advocate for biologically and evolutionarily meaningful character analysis. He has published about 200 articles, six monographs, and six books on this subject. This book features subjects such as the evolution and adaptation of mammals and provides up-to-date articles on the evolutionary morphology of a wide range of mammalian groups.
Author | : Liam J. Revell |
Publisher | : Princeton University Press |
Total Pages | : 441 |
Release | : 2022-07-12 |
Genre | : Science |
ISBN | : 0691219044 |
An authoritative introduction to the latest comparative methods in evolutionary biology Phylogenetic comparative methods are a suite of statistical approaches that enable biologists to analyze and better understand the evolutionary tree of life, and shed vital new light on patterns of divergence and common ancestry among all species on Earth. This textbook shows how to carry out phylogenetic comparative analyses in the R statistical computing environment. Liam Revell and Luke Harmon provide an incisive conceptual overview of each method along with worked examples using real data and challenge problems that encourage students to learn by doing. By working through this book, students will gain a solid foundation in these methods and develop the skills they need to interpret patterns in the tree of life. Covers every major method of modern phylogenetic comparative analysis in R Explains the basics of R and discusses topics such as trait evolution, diversification, trait-dependent diversification, biogeography, and visualization Features a wealth of exercises and challenge problems Serves as an invaluable resource for students and researchers, with applications in ecology, evolution, anthropology, disease transmission, conservation biology, and a host of other areas Written by two of today’s leading developers of phylogenetic comparative methods
Author | : Francesco de Bello |
Publisher | : Cambridge University Press |
Total Pages | : 311 |
Release | : 2021-03-11 |
Genre | : Nature |
ISBN | : 1108472915 |
Trait-based ecology is rapidly expanding. This comprehensive and accessible guide covers the main concepts and tools in functional ecology.
Author | : Laura C. Soul |
Publisher | : Cambridge University Press |
Total Pages | : 77 |
Release | : 2021-05-27 |
Genre | : Science |
ISBN | : 1108897355 |
Recent advances in statistical approaches called phylogenetic comparative methods (PCMs) have provided paleontologists with a powerful set of analytical tools for investigating evolutionary tempo and mode in fossil lineages. However, attempts to integrate PCMs with fossil data often present workers with practical challenges or unfamiliar literature. This Element presents guides to the theory behind and the application of PCMs with fossil taxa. Based on an empirical dataset of Paleozoic crinoids, example analyses are presented to illustrate common applications of PCMs to fossil data, including investigating patterns of correlated trait evolution and macroevolutionary models of morphological change. The authors emphasize the importance of accounting for sources of uncertainty and discuss how to evaluate model fit and adequacy. Finally, the authors discuss several promising methods for modeling heterogeneous evolutionary dynamics with fossil phylogenies. Integrating phylogeny-based approaches with the fossil record provides a rigorous, quantitative perspective on understanding key patterns in the history of life.
Author | : Ziheng Yang |
Publisher | : Oxford University Press, USA |
Total Pages | : 374 |
Release | : 2006-10-05 |
Genre | : Medical |
ISBN | : 0198566999 |
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.
Author | : Jeffrey R. Thompson |
Publisher | : Cambridge University Press |
Total Pages | : 120 |
Release | : 2022-12-01 |
Genre | : Science |
ISBN | : 1009189190 |
The echinoderms are an ideal group to understand evolution from a holistic, interdisciplinary framework. The genetic regulatory networks underpinning development in echinoderms are some of the best known for any model group. Additionally, the echinoderms have an excellent fossil record, elucidating in in detail the evolutionary changes underpinning morphological evolution. In this Element, the echinoderms are discussed as a model group for molecular palaeobiological studies, integrating what is known of their development, genomes, and fossil record. Together, these insights shed light on the molecular and morphological evolution underpinning the vast biodiversity of echinoderms, and the animal kingdom more generally.
Author | : László Zsolt Garamszegi |
Publisher | : Springer |
Total Pages | : 553 |
Release | : 2014-07-29 |
Genre | : Science |
ISBN | : 3662435500 |
Phylogenetic comparative approaches are powerful analytical tools for making evolutionary inferences from interspecific data and phylogenies. The phylogenetic toolkit available to evolutionary biologists is currently growing at an incredible speed, but most methodological papers are published in the specialized statistical literature and many are incomprehensible for the user community. This textbook provides an overview of several newly developed phylogenetic comparative methods that allow to investigate a broad array of questions on how phenotypic characters evolve along the branches of phylogeny and how such mechanisms shape complex animal communities and interspecific interactions. The individual chapters were written by the leading experts in the field and using a language that is accessible for practicing evolutionary biologists. The authors carefully explain the philosophy behind different methodologies and provide pointers – mostly using a dynamically developing online interface – on how these methods can be implemented in practice. These “conceptual” and “practical” materials are essential for expanding the qualification of both students and scientists, but also offer a valuable resource for educators. Another value of the book are the accompanying online resources (available at: http://www.mpcm-evolution.com), where the authors post and permanently update practical materials to help embed methods into practice.
Author | : Colin D. Sumrall |
Publisher | : Cambridge University Press |
Total Pages | : 91 |
Release | : 2023-04-13 |
Genre | : Science |
ISBN | : 1009397168 |
The extraxial-axial theory (EAT) and universal elemental homology (UEH) are often portrayed as mutually exclusive hypotheses of homology within pentaradiate Echinodermata. EAT describes homology upon the echinoderm bauplan, interpreted through early post-metamorphic growth and growth zones, dividing it into axial regions generally associated with elements of the ambulacral system and extraxial regions that are not. UEH describes the detailed construction of the axial skeleton, dividing it into homologous plates and plate series based on symmetry, early growth, and function. These hypotheses are not in conflict; the latter is rooted in refinement of the former. Some interpretive differences arise because many of the morphologies described from eleutherozoan development are difficult to reconcile with Paleozoic forms. Conversely, many elements described for Paleozoic taxa by UEH, such as the peristomial border plates, are absent in eleutherozoans. This Element recommends these two hypotheses be used together to generate a better understanding of homology across Echinodermata.