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First life-forms appeared at least as early as 3.5 billion years ago in the form of prokaryotes. Some of these species developed oxygenic photosynthesis, which resulted in the presence of oxygen gas in the atmosphere. Later, eukaryotes appeared and diversified through mutation and gene duplication (including mutation and duplication of master genes), which led to the rewiring of entire gene networks. The chapter shows that there is no fundamental difference between macroevolution and microevolution. It shows that making artificial life in the lab as well as transgenic life-forms would be impossible if the Intelligent Design scenario were correct. Indeed, ID posits that living systems were holistically designed and thus cannot be constructed in a piecemeal fashion.

The Dollo parsimony method is based on the assumption that a complex character that has been lost during evolution of a particular lineage cannot be regained. When applicable, this principle leads to a substantial simplification of evolutionary analysis and provides for unambiguous reconstruction of evolutionary scenarios, which may not be attainable with other methods. In this chapter, applications of Dollo parsimony are described for the quantitative analysis of the dynamics of genome evolution. Dollo parsimony is the method of choice for reconstructing evolution of the gene repertoire of eukaryotic organisms because although multiple, independent losses of a gene in different lineages are common, multiple gains of the same gene are improbable. This contrasts with the situation in prokaryotes where the widespread occurrence of horizontal gene transfer makes multiple gains possible, thereby invalidating the Dollo principle. The chapter applies Dollo parsimony to reconstruct the scenario of evolution for the genomes of crown-group eukaryotes by assigning the loss of genes and emergence of new genes to the branches of the phylogenetic tree, and delineate the minimal gene sets for various ancestral forms. A similar analysis, with rather unexpected results, was performed to infer gain versus loss of introns in conserved eukaryotic genes. The applicability of the Dollo principle for these and other problems in evolutionary genomics is discussed.

While traditionally ecology textbooks only discuss the short term carbon cycle, the role of life has been crucial in the geological long term carbon cycle through processes such as silicate weathering. Arguments have been put forward for the co-evolution of CO₂ levels and terrestrial plants — with adaptations to lower CO₂ levels allowing large leaves to evolve. It seems clear that on Earth without the effect of life our planet would currently have a temperature which would rule out he survival of eukaryotic life. This suggests that carbon sequestration has a positive Gaian effect. However, this is probably a local conclusion which cannot be generalized to all other planets. More generally, these ideas illustrate the importance of biomass as a key feature of global ecologies. The effects of vegetation (or plankton) on carbon cycles are more directly linked to available biomass than species richness.

This chapter provides a three-part introduction to sex differences, stressing both the conserved and the unique as part of Darwin's notion of descent with modification. The first section takes a step back in time and provides a broad perspective on the evolution of eukaryotes. The evolution of meiosis and syngamy (i.e., the fusion of two cells) was a precondition for the evolution of dimorphic gametes and the subsequent evolution of all other sex differences. It then outlines general causes of sex differences in animals by focusing on natural and sexual selection. The second section discusses the mechanisms that underlie sex differences in gene expression as well as the basic developmental mechanisms that produce sex differences. The third section reviews some elegant research that links evolutionary causes of and proximate mechanisms for sex differences in the brain and behavior. These examples show how sex-specific selection on behavior ultimately drives neural evolution. The chapter concludes by briefly outlining what is known about sexual differentiation of neural mechanisms in humans.

This chapter focuses on how yeast became the prime focus of eukaryotic molecular biology after 1975. It summarizes some of the major studies in yeast biology. It shows how progress in disentangling the complexity of certain features of the eukaryotic cell enabled yeast to supplant the filamentous fungi definitively as a model eukaryote.

This chapter traces the development of the baker's and brewer's yeast known now as Saccharomyces cerevisiae as a model organism. In particular, it discusses studies by Øjvind Winge, Carl Lindegren, and Boris Ephrussi.

By the early 1990s, it was becoming clear that the commonly used five kingdom classification schemes were oversimplified and simply inadequate for describing the major divisions of life. At this critical point in time, when morphological data from electron microscopy was beginning to be supplemented with information from DNA sequences, Chris Humphries organized a Linnean Society conference entitled “Modern Views of Kingdoms and Domains” in the spring of 1994 to discuss the new, emerging picture of eukaryotic relationships. This chapter reviews the general history of the debate over the eukaryote tree of life and describes the progress that has been made since that historic conference. When Carl Linnaeus presented the catalog of all life using his binomial system of nomenclature in 1758, he described two kingdoms: Plantae and Animalia. The unicellular eukaryotes were discovered approximately 300 years ago by Antony van Leeuwenhoek, who considered them to be tiny animals that he called simply “animalcules.” This chapter also describes Opisthokonta, Amoebozoa, Archaeplastida, alveolates and stramenopiles, Rhizaria, and excavates.

This chapter reviews the literature on speciation experiments, identifies neglected questions that could be addressed by new experiments, and suggests general guidelines for such experiments, focusing exclusively on sexually reproducing eukaryotes—that is, those with meiosis and syngamy at some stage of the life cycle. It first defines key concepts used in the speciation literature and gives an overview of the questions that have been, or could be, addressed by experimental evolution approaches. The chapter then suggests questions that have been mostly neglected in past experiments, but which are ripe for further investigation, and finally gives some general guidelines for future laboratory experiments on speciation.

This chapter describes evolution as a long-running algorithm that has designed all species on Earth. Evolution, a process discovered by Charles Darwin, has been working for more than four billion years to obtain, at first, simple unicellular organisms (prokaryotes) and, later, much more complex life forms, based on eukaryotic cells. Evolution worked not with bits stored in a computer memory, but with replicators that are digital sequences written in very long DNA molecules, the genomes. Complex cells, which are the results of this optimization algorithm, eventually organized themselves in vast multi-cellular complexes, leading to the multicellular organisms in existence today and, ultimately, to humans and the human brain, the most complex information processing device we know.

This chapter explains what the book is about and highlights the range of processes and questions to be considered. The central thesis is that species represent more than a unit of taxonomy, they are a model of how diversity is structured and how groups of organisms evolve. All organisms live in diverse communities with hundreds of other species. Knowledge of what species are, how they form, and the genetic and ecological interactions among them is therefore vital both for understanding where diversity comes from and for predicting contemporary and future evolution. It is time for evolutionary biology to embrace the diversity of life.

Ever since life’s debut on the earth, biotic evolution has been a near-balancing act. On virtually every level, competition and cooperation, shifting endlessly between foreground and background, have tugged and teased evolving systems as they have wobbled through time along the edge of chaos. The emergence of cellular life from the world of complex carbon-based chemistry appears to have happened only once in the primordial dreamtime of planet Earth. Scientists base this conjecture on a number of virtually universal distributions of chemical structures and processes across the spectrum of living organisms. Despite their perhaps tenuous hold on life, the earliest cells, primitive bacteria and archea, possessed the keys to the opening of new potential for matter and energy—the capabilities of self-replication, controlled energy transduction, directed locomotion, and the regulation of an internal environment. Out of this cellular Big Bang there arose a totally new force field on planet Earth superimposed over the physical, chemical, and geological, but with tendrils pervading all of those realms. It was the beginning of the biosphere. Life pervaded and began to transform the lithosphere, hydrosphere, and atmosphere. The chapter highlights transitions of prokaryote to eukaryote via endosymbiosis. Also featured are: biofilms, bioluminescence, coral reefs, and ecological succession.

Due to its extensive deep-time history encompassing almost 600 million years, the fossil record offers important insights into changing biodiversity in marine ecosystems, inluding rapid diversification during the radiation of metazoans in the Ediacaran and the Cambrian explosion. This chapter examines three key biodiversity changes in history: the Ediacaran radiation of large multicellular eukaryotes, the Cambrian radiation of complex bilaterian-grade animals, and the end-Permian mass extinction. It discusses changes in biodiversity and their relation to various factors involved in ecosystem functioning such as bioturbation (biogenic mixing depth), functional diversity, and productivity. It also considers the link between species richness and functional diversity, the productivity-biodiversity relationship, and environmental changes during the late Paleozoic to early Mesozoic.

This chapter develops a subtle model that integrates environmental and internal factors. It describes the phylogenetic distribution of multicellular organisms in general and complex multicellular life in particular, clarifying the important distinction between the two. This chapter shows that the long apparent lag between the appearance of simple multicellularity in eukaryotes and the radiation of groups with complex multicellular organization has an environmental component that can be associated back to the consequences of life with interior and exterior cells. It suggests that the evolutionary transition from unicells to complex multicellular organisms has several steps.

The chapter starts with a history of archaeal genomic and continue discussing the impact of genomic revolution on the author’s work and on several critical evolutionary issues. Notably, comparative genomic associated to phylogenetic analyses, revealed that reverse gyrase is the only protein specific for hyperthermophiles and was probably not present in LUCA, again suggesting a cold LUCA. Many molecular features are common to archaea and eukaryotes. To illustrate this point, the author explains how the discovery of a new family of DNA topoisomerase in archaea allowed him to identify a protein at the origin of eukaryotic sex, which also determines the size of plants! The role of bioinformatics in modern biology is emphasised, with spotlight on Eugene Koonin, a major actor in the field. In the last sections, the author presents arguments against the popular idea that eukaryotes emerged from the engulfment of a bacterium by an archaeon. This scenario was recently boosted by the reconstruction from metagenomic data of the genomes of new archaea, such as the Lokiarchaea, supposed to be sister groups of eukaryotes. The author reported recent results from his laboratory showing that this is probably not the case and supporting the classical Woese’s tree of life.