Timetrees Incorporating Fossils And Molecules 2nd Edition
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Timetrees: Incorporating Fossils and Molecules, 2nd edition
Calibrating phylogenies to time is central to addressing many questions in evolutionary biology and macroevolution. The fossil record once provided our only source for establishing a timeline for evolution. However, the incompleteness of the fossil record and the non-uniformity of fossil recovery rate make it challenging to obtain precise estimates of divergence times from fossil evidence alone. Molecular dating, which combines evidence from the geological and molecular records, enables us to generate a much more complete and precise timeline of events. The molecular clock can be time-calibrated using temporal evidence from fossils and used to estimate divergence times based on the assumption that the rate of sequence evolution will be approximately constant over time and among lineages. Methodological challenges to applying this concept in practice have been to relax the assumption of constant evolutionary rates and to model the uncertainty associated with paleontological and geological calibrations. To this end, available statistical methods have become increasingly complex in order to capture key features of empirical data. These are typically applied using Bayesian inference, which provides a powerful framework for incorporating multiple sources of uncertainty. Although overall more effort has been expended in developing models of molecular sequence evolution, critical advances have also included approaches to modeling taxonomic diversification and fossilization. In particular, recent advances in birth-death process models have allowed for continuous sampling along lineages, enabling more information from the fossil record to be incorporated into dating analyses in a statistically coherent way. In addition, available dating methods can now be applied to scenarios in which no molecular data may be available, allowing for novel insights into the evolution of entirely extinct clades. Other recent innovations enable us to date divergence times among taxa that have no fossil record, including the use of gene duplication events or biogeographic evidence. Furthermore, time-calibrated trees are necessary for obtaining phylogenetic estimates of taxonomic diversification and extinction rates, which can now be jointly inferred along with lineage divergence times. These approaches offer an exciting opportunity to understand the evolution of life in deep time, although key challenges remain, especially with regards to modeling the processes of genome evolution, taxonomic diversification and fossil recovery. In this Research Topic, we focus on recent advances in methodology, outstanding challenges, and the application of molecular and paleontological dating methods to empirical case studies across the Tree of Life.
The Timetree of Life
The evolutionary history of life includes two primary components: phylogeny and timescale. Phylogeny refers to the branching order (relationships) of species or other taxa within a group and is crucial for understanding the inheritance of traits and for erecting classifications. However, a timescale is equally important because it provides a way to compare phylogeny directly with the evolution of other organisms and with planetary history such as geology, climate, extraterrestrialimpacts, and other features.The Timetree of Life is the first reference book to synthesize the wealth of information relating to the temporal component of phylogenetic trees. In the past, biologists have relied exclusively upon the fossil record to infer an evolutionary timescale. However, recent revolutionary advances in molecular biology have made it possible to not only estimate the relationships of many groups of organisms, but also to estimate their times of divergence with molecular clocks. The routineestimation and utilization of these so-called 'time-trees' could add exciting new dimensions to biology including enhanced opportunities to integrate large molecular data sets with fossil and biogeographic evidence (and thereby foster greater communication between molecular and traditional systematists). Theycould help estimate not only ancestral character states but also evolutionary rates in numerous categories of organismal phenotype; establish more reliable associations between causal historical processes and biological outcomes; develop a universally standardized scheme for biological classifications; and generally promote novel avenues of thought in many arenas of comparative evolutionary biology.This authoritative reference work brings together, for the first time, experts on all major groups of organisms to assemble a timetree of life. The result is a comprehensive resource on evolutionary history which will be an indispensable reference for scientists, educators, and students in the life sciences, earth sciences, and molecular biology. For each major group of organism, a representative is illustrated and a timetree of families and higher taxonomic groups is shown. Basic aspects ofthe evolutionary history of the group, the fossil record, and competing hypotheses of relationships are discussed. Details of the divergence times are presented for each node in the timetree, and primary literature references are included. The book is complemented by an online database(www.timetree.net) which allows researchers to both deposit and retrieve data.
Phylonyms
Phylonyms is an implementation of PhyloCode, which is a set of principles, rules, and recommendations governing phylogenetic nomenclature. Nearly 300 clades - lineages of organisms - are defined by reference to hypotheses of phylogenetic history rather than by taxonomic ranks and types. This volume will document the Real World uses of PhyloCode and will govern and apply to the names of clades, while species names will still be governed by traditional codes. Key Features Provides clear regulations for implementing new guidelines for naming lineages of organisms incorporates expressly evolutionary and phylogenetic principles Works with existing codes of nomenclature Eliminates the reliance on rank-based classification in favor of phylogenetic relationships Related Titles: Rieppel, O. Phylogenetic Systematics: Haeckel to Hennig (ISBN 978-1-4987-5488-0) Cantino, P. D. and de Queiroz, K. International Code of Phylogenetic Nomenclature (PhyloCode) (ISBN 978-1-138-33282-9).