The Phylogenetic Handbook is a broad, hands on guide to theory and practice of nucleotide and protein phylogenetic analysis. This second edition includes six new chapters, covering topics such as Bayesian inference, tree topology testing and the impact of recombination on phylogenies, as well as a detailed section on molecular adaptation. The book has a stronger focus on hypothesis testing than the previous edition, with more extensive discussions on recombination analysis, detecting molecular adaptation and genealogy-based population genetics. Many chapters include elaborate practical sections, which have been updated to introduce the reader to the most recent versions of sequence analysis and phylogeny software, including BLAST, FastA, Clustal, T-coffee, Muscle, DAMBE, Tree-puzzle, Phylip, MEGA, PAUP*, IQPNNI, CONSEL, ModelTest, Prottest, PAML, HYPHY, MrBayes, BEAST, LAMARC, SplitsTree, and RDP. Many analysis tools are described by their original authors, resulting in clear explanations that constitute an ideal teaching guide for advanced-level undergraduate and graduate students.

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This book contains an overview of research on the interaction of biological and sociological processes. Issues explored include: the origins of social solidarity; religious beliefs; sex differences; gender inequality; human happiness; social stratification and inequality; identity, status, and other group processes; race, ethnicity, and discrimination; fertility and family processes; crime and deviance; cultural and social change.

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.

This Special Issue on the Systematics and Phylogeny of Weevils presents 31 new research papers on one of the most diverse and successful groups of animals on Earth, the beetle superfamily Curculionoidea. It was in part inspired to commemorate the extraordinary life and scientific achievements of Guillermo (“Willy”) Kuschel (1918–2017), who shaped this field of science over the last century like no other weevil systematist. The papers in this memorial issue span weevil faunas from all over the globe, including South and Central America, Africa, Europe and the Near East, South-East Asia, New Guinea, Australia and New Zealand. They include major advances on the phylogeny and classification of the “broad-nosed” weevils (Entiminae), on the weevils associated with American cycads and on the unique extinct weevil fauna preserved in the 100-million-year-old Burmese amber, when weevils started to diversify alongside the oldest angiosperm plants. They comprise a tribute to Willy Kuschel, the proceedings of a weevil symposium held in his honor in 2016 in Orlando, Florida, 24 systematic studies (including seven phylogenetic analyses) and five other contributions on the diversity, biology, distribution, evolution and fossil history of weevils. In the papers collated in this volume, 30 new genera and 92 new species of weevils are described and a new family of extinct weevils is recognized.

The evolutionary history of species is traditionally represented using a rooted phylogenetic tree. However, when reticulate events such as hybridization, horizontal gene transfer or recombination are believed to be involved, phylogenetic networks that can accommodate non-treelike evolution have an important role to play. This book provides the first interdisciplinary overview of phylogenetic networks. Beginning with a concise introduction to both phylogenetic trees and phylogenetic networks, the fundamental concepts and results are then presented for both rooted and unrooted phylogenetic networks. Current approaches and algorithms available for computing phylogenetic networks from different types of datasets are then discussed, accompanied by examples of their application to real biological datasets. The book also summarises the algorithms used for drawing phylogenetic networks, along with the existing software for their computation and evaluation. All datasets, examples and other additional information and links are available from the book's companion website at www.phylogenetic-networks.org.

This book is about phylogenetic diversity as an approach to reduce biodiversity losses in this period of mass extinction. Chapters in the first section deal with questions such as the way we value phylogenetic diversity among other criteria for biodiversity conservation; the choice of measures; the loss of phylogenetic diversity with extinction; the importance of organisms that are deeply branched in the tree of life, and the role of relict species. The second section is composed by contributions exploring methodological aspects, such as how to deal with abundance, sampling effort, or conflicting trees in analysis of phylogenetic diversity. The last section is devoted to applications, showing how phylogenetic diversity can be integrated in systematic conservation planning, in EDGE and HEDGE evaluations. This wide coverage makes the book a reference for academics, policy makers and stakeholders dealing with biodiversity conservation.

This book serves as a brief introduction to phylogenetic trees and molecular evolution for biologists and biology students. It does so by presenting the main concepts in a variety of ways: first visually, then in a history, next in a dice game, and finally in simple equations. The content is primarily designed to introduce upper-level undergraduate and graduate students of biology to phylogenetic tree reconstruction and the underlying models of molecular evolution. A unique feature also of interest to experienced researchers is the emphasis on simple ways to quantify the uncertainty in the results more fully than is possible with standard methods.

Issues in multilingualism and its implications for communities and society at large, language acquisition and use, language diversification, and creative language use associated with new linguistic identities have become hot topics in both scientific and popular debates. A ubiquitous aspect of multilingualism is language contact. This book contains twelve articles that discuss specific aspects of Contact Linguistics. These articles cover a wide range of topics in the field, including creoles, areal linguistics, language mixing, and the sociolinguistic aspects of interactions with audiences. The book is dedicated to Pieter Muysken whose work on pidgin and creole languages, mixed languages, code-switching, bilingualism, and areal linguistics has been ground-breaking and inspirational for the authors in this book, as well as numerous other scholars working on the various facets of this rapidly expanding field.

Genetics and Evolution of Infectious Diseases is at the crossroads between two major scientific fields of the 21st century: evolutionary biology and infectious diseases. The genomic revolution has upset modern biology and has revolutionized our approach to ancient disciplines such as evolutionary studies. In particular, this revolution is profoundly changing our view on genetically driven human phenotypic diversity, and this is especially true in disease genetic susceptibility. Infectious diseases are indisputably the major challenge of medicine. When looking globally, they are the number one killer of humans and therefore the main selective pressure exerted on our species. Even in industrial countries, infectious diseases are now far less under control than 20 years ago. The first part of this book covers the main features and applications of modern technologies in the study of infectious diseases. The second part provides detailed information on a number of the key infectious diseases such as malaria, SARS, avian flu, HIV, tuberculosis, nosocomial infections and a few other pathogens that will be taken as examples to illustrate the power of modern technologies and the value of evolutionary approaches. Takes an integrated approach to infectious diseases Includes contributions from leading authorities Provides the latest developments in the field