The increasing availability of molecular and genetic databases coupled with the growing power of computers gives biologists opportunities to address new issues, such as the patterns of molecular evolution, and re-assess old ones, such as the role of adaptation in species diversification. In the second edition, the book continues to integrate a wide variety of data analysis methods into a single and flexible interface: the R language. This open source language is available for a wide range of computer systems and has been adopted as a computational environment by many authors of statistical software. Adopting R as a main tool for phylogenetic analyses will ease the workflow in biologists' data analyses, ensure greater scientific repeatability, and enhance the exchange of ideas and methodological developments. The second edition is completed updated, covering the full gamut of R packages for this area that have been introduced to the market since its previous publication five years ago. There is also a new chapter on the simulation of evolutionary data. Graduate students and researchers in evolutionary biology can use this book as a reference for data analyses, whereas researchers in bioinformatics interested in evolutionary analyses will learn how to implement these methods in R. 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: manipulation of phylogenetic data, phylogeny estimation, tree drawing, phylogenetic comparative methods, and estimation of ancestral characters. 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.
Biologists, some with specialties, and a paleontologist summarize research on selected topics relating to using a phylogenetic framework to understand how plants and animals, their traits, and interactions between species evolve. The eight studies are from the 1996 symposium Morphological Data in Phylogenetic Analysis: Recent Progress and Unresolved Problems, held in St. Louis, Missouri. Annotation copyrighted by Book News, Inc., Portland, OR
Neotropical ichthyology: an overview; Fossils and geological evidence; The stage for neotropical fish diversification: a history of tropical south american rivers; The temporal context for the diversification of neotropical fishes; Phylogeny of fossil characiformes and paleobiogeography of the Tremembe formation, Sao Paulo; Brazil; Maastrichtian to early late paleocene freshwater osteichthyes of Bolivia: additions and comments; Characiformes; Higher lever phylogenetic concepts within characiforms (Ostariophysi), a historical review; Relationships of the characidiinae and phylogeny of characiform fishes (Teleostei: ostariophysi); Phylogenetic study of the hemiodontidae (Ostariophysi: characiformes); Perspectives about the phylogeny and classification of the chacidae (Teleostei: Characiformes); Relationships of the tribes and genera of the glandulocaudinae (Ostariophysi: characiformes: characidae) with a description of a New Genus, Chrysobrycon; Monophyly of the Cheirodontinae, characters and major clades (Ostariophysi: characidae); Sperm ultrastructure in characid fishes (Teleostei: ostariophysi); The genus Creagrutus (Teleostei: Characiformes: Characidae): monophyly, relationships, and undetected diversity; A phylogenetic analysis of Roestes Gunther and Gilbertolus Eigenmann, with a hypothesis on the relationships of the Cynodontidae and Acestrorhynchidae (Teleostei: Ostariophysi: Characiformes); Siluriformes; Phylogenetic relationships of neotropical siluriformes: historical overview and synthesis of hypotheses; Monophyly and interrelationships of the Centromochlinae (Siluriformes: Auchenipteridae); Systematics, biogeography, and the fossil record of the Callichthyidae: a review of the available data; Phylogenetic relationships of the Loricariidae (Siluriformes) based on mitochondrial rRNA gene sequences; Conflict and resolution: impact of new taxa on phylogenetic studies of the neotropical cascudinhos (Siluroidei: Loricariidae); Gymnotiformes; The Gymnotiform "Eels" of tropical America: a history of classification and phylogeny of the South American electric Knifefishes (Teleostei: Ostariophysi: Siluriphysi); Phylogenetic systematics of Gymnotiformes with diagnoses of 58 clades: a review of available data; The phylogenetic position of the South America Electric Fish genera Sternophygus and Archolaemus (Ostariophysi: Gymnotiformes) according to 12s and 16s mitochondrial DNA sequences; Perciformes; A phylogeny and classfication of the South American Cichlidae (Teleostei: Perciformes); Molecular phylogeny of neotropical cichlids: the relationships of Cichlasomines and heroines; Mitochondrial phylogenetics, biogeography, and evolution of parental care and mating systems in Gymnogeophagus (Perciformes: Cichlidae); Atherinomorpha; Phylogenetic systematics and historical biogeography of the neotropical silverside family Atheronopsidae (Teleostei: Atheriniformes); Phylogeny and classification of the Cyprinodontiformes (Euteleostei: Atherinomorpha): a reappraisal; Phylogeny and classification of the Anablepidae (Teleostei: Cyprinodontiformes); Cytogenetic markers; Cytogenetic markers in neotropical freshwater fishes.