Principles of Evolution

Systems, Species, and the History of Life

Jonathan Bard

• Publisher: Garland Science
• Year: 2016
• ISBN:
  9781351854764
• Edition: 1
• Topic: Biological Sciences
• Subtopic: Evolution
• Index: Biological Sciences

Principles of Evolution covers all aspects of the subject. Following an introductory section that provides necessary background, it has chapters on the evidence for evolution that cover the fossil record, DNA-sequence homologies, and protein homologies (evo-devo). It also includes a full history of life from the first universal common ancestor, through the rise of the eukaryote and on to the major groups of phyla. This section is followed by one on the mechanism of evolution with chapters on variation, selection and speciation. The main part of the book ends with a chapter on human evolution and this is followed by appendices that expand on the making of fossils, the history of the subject and creationism.

What marks this book as different from others on evolution is its systems-biology perspective. This new area focuses on the role of protein networks and on multi-level complexity, and is used in three contexts. First, most biological activity is driven by such networks and this has direct implications for understanding evo-devo and for seeing how variation is initiated, mainly during embryogenesis. Second, it provides the natural language for discussing phylogenetics. Third, evolutionary change involves events at levels ranging from the genome to the ecosystem and systems biology provides a context for integrating material of this complexity.

The book assumes a basic grounding in biology but little mathematics as the difficult subject of evolutionary population genetics is mainly covered qualitatively, with major results being discussed and used rather than derived. Principles of Evolution will be an interesting and thought-provoking text for undergraduates and graduates across the biological sciences.

SECTION 1
AN INTRODUCTION TO EVOLUTION

This first section aims to provide sufficient background for the reader to understand the science behind the evidence for evolutionary change (Section 2) and the work that has unraveled the mechanisms by which that change occurs (Section 3). Many readers will know some of this material and should feel free to browse through these early chapters or just use them for reference.

Chapter 1 is an introduction that attempts to do no more than set the context for approaching evolution and the perspective from which this book is written. A particular focus here is systems biology; this is a new area of biology, one of whose aims is to explore the properties and roles of the complex protein networks that drive much of development in the embryo and physiology in the adult. It is important in any study of evolution because variation and change usually derive from mutations that affect the properties of these networks. More information on systems biology is given in Appendix 1.

Some basic history (Chapter 2) is required to provide the context for understanding how our current knowledge of evolution was achieved, why different problems were worth working on at different times, and how one area of the subject built on others. This chapter is very short, and interested readers can find more detail on this fascinating subject in Appendix 2.

The key problem in evolution, as Darwin realized, is how new species evolve from existing ones. Exploring this requires appreciating how species are recognized and how they are organized. Chapter 3 discusses today’s current diverse range of organisms and how they are taxonomically grouped on the basis of their properties. In a sense, this chapter asks the questions that the rest of the book has to answer.

CHAPTER 1
APPROACHING EVOLUTION

This first short chapter discusses the approach that this book takes to investigating the detail of evolution.

Our planet teems with life. In the sky, on the land, in the sea, and in between, there are some millions of species of plants, animals, fungi, bacteria, and viruses, and almost all thrive as they develop and reproduce using energy directly or indirectly derived from the sun. This is possible because each species is appropriately adapted to the environment in which it lives: its ecosystem provides it with food, and it, in turn, provides nourishment and a context for other organisms, sometimes while it lives and always when it dies. Unicellular organisms, be they prokaryotic or eukaryotic, can reproduce by simple division, whereas multicellular organisms mainly reproduce by mating – no multicellular individual survives or reproduces in the long term unless it is part of a population.

The key purpose of the science of evolution is to make sense of this richness, to understand how it arose, to track the diversity of life backwards in time to its origins, and to study the mechanisms by which that diversity evolved and continues to evolve, always ensuring that species adapt to their environment. The data required for this enterprise come from across the whole of biology, and include information from contemporary and fossilized organisms, molecular biology and cytogenetics, comparative embryology, comparative genomics, and even from the comparison of the two gene sequences in a particular pair of chromosomes in a diploid individual. It is worth noting that, other than this last example, evidence from an individual organism or even the most wonderful of fossils, rarely represents more than just an interesting fact in this context. The science of evolution mainly deals with interpreting comparisons of data from and relationships among species.

Such comparisons are, however, just the start: understanding evolutionary change requires a much broader approach because all organisms live and evolve in a rich and complex biological and physical environment, and have always done so. Whether a species thrives or dies out depends on its interactions with that environment. What we know about that species, in particular, and evolutionary biology, in general, depends on ecology and even the climate as much as on genomics.

We would, of course, love to study evolution directly, but we cannot: eukaryotic speciation generally requires perhaps a million generations and, for larger species, even more millions of years for mutation to generate and for the environment to select a new population that is recognized as a novel and distinct species. Heritable change to an organism’s phenotype is usually far too slow to be appreciated in the here and now; therefore, research work has to be indirect.

It is sometimes claimed that, unlike physics, biology does not have any profound theories. Physics, however, requires four forces and many, many laws about how they operate to explain the world of particles and inanimate objects. What is unusual about biology, compared with physics and, indeed, all other areas of science, is that it has a single underlying concept that integrates so much of its subject matter. This concept is that novel species evolve from existing ones through environmental or natural selection acting on heritable variants, with the result being that new species form through descent with modification – this is evolution. Darwin had this deep insight into how evolutionary change happens around the 1840s but only published it some 15 years later in his masterwork On the Origin of Species, an 1859 classic that is still worth reading. Darwin’s single insight provides the framework within which it is possible to discuss the whole of life, from its simple beginnings to now.

A systems biology perspective

This is a book whose main underlying focus is on speciation, or the mechanisms by which new species form from existing ones. As Darwin realized more than 150 years ago, this is the key problem in evolution and this is because the reproductive isolation of a new species is a one-way route to further diversification. At the macroscopic level, a great deal is known about speciation, but the molecular details are still opaque because it is a long way from a mutation in the DNA that affects the structure or expression details of a protein to a downstream change in anatomy or behavior that eventually helps to produce reproductive isolation. While a fair amount is understood about the mechanisms that form normal tissues, knowledge of the effects of mutations that have minor effects on these mechanisms, rather than just blocking them, is very limited. This is because a minor change in a protein sequence rarely has an obvious advantageous effect on the rich and complex phenotype of an organism.

Perhaps the major advances in biological thinking over the last decade have been in the area of systems biology (Noble, 2008), a subject whose roots come from the realization that many proteins do not work alone but co-operate within networks that produce a single functional output, one that could rarely have been predicted on the basis of the role of any of its individual proteins. This realization has changed how we think about the relationship between the genotype and the phenotype, particularly with respect to the effects of mutation (Capra & Luisi, 2014). Systems biologists are also grappling with the nature of biological complexity, particularly through the ways in which events at different levels interact through feedback and hence how causality is distributed. The analysis of protein networks reflects a narrow view of systems biology, while the study of complexity across levels and systems requires a broader approach (Bard, 2013a). Some of the basic ideas of systems biology and its formal language are discussed in Appendix 1.

The most obvious area of evolution where systems biology in the narrow sense matters is in evo-devo, the area that investigates molecular similarities in the development of very different organisms. As far back as the 1970s, it had become clear that proteins such as cytochrome C, which has similar functions in very different organisms, had amino acid sequences that could be seen as deriving from a common ancestor (they were homologs). By the 1980s, many other examples had been discovered where homologous proteins played the same key role in the development of very different organisms. A good example is the Pax6 protein: this transcription factor lies at the base of the hierarchy of mechanisms responsible for eye development across the phyla to the extent that the Pax6 protein, whose activity initiates the development of the camera eye in the mouse, can substitute for its homolog in Drosophila and initiate a compound eye in the fly (Gehring, 1996).

More recently, it has become apparent that such homologies extend upwards to the next level of molecular organization, that of protein networks, where very similar networks have much the same roles in very different organisms (Gilbert, 2014). Across development, homologous pathways and networks often control signaling, patterning, differentiation, cell division, and cell death, as well as morphogenesis in different phyla (Chapters 10 & 11). Knowledge of the programmed cell death (apoptosis) pathway in mammals, for example, derived from identifying homologs of proteins first discovered in the developing nematode worm, Caenorhabditis elegans. Such networks are important in two evolutionary contexts: first, the fact that there are such homologies across the phyla is strong evidence for very different species sharing a last common ancestor; second, anatomical variation, the basic driver of evolutionary change, comes from mutations that modulate the output of these networks, particularly those that control patterning and growth. Systems biology, in the narrow sense of understanding how protein networks generate their outputs, is at the very heart of evolutionary thinking.

While the effect of a mutation on the function of an individual protein can often be straightforward and even measurable in vitro, the effect of that mutated protein on the output of a complex network in which it participates is usually impossible to predict, unless, of course, the mutation causes that network to fail. It is even harder to predict the downstream effect of the original mutation on that organism’s phenotype, other than that it may produce an anatomical or physiological variant in the organism that should be heritable. Such phenotypic change is, however, only the beginning of speciation. Whether that change is worth maintaining depends on selection and this, in turn, depends on the local environment, an umbrella term that covers the effects of population pressure and competition from the original and other organisms, the climate, food availability, and, indeed, anything that affects reproductive success. Not only are the events within an individual level complicated, but there are also interactions between levels: population numbers depend on climate and food, while phenotypic variants need to be able to reproduce with other members of their species.

This sense of levels and the interactions between them is captured in the theory of evolutionary population genetics (the modern evolutionary synthesis), which was developed around 1925–45. This theory describes how the frequencies of subpopulations of variants within a population change due to to natural selection, genetic drift, and other factors (Chapter 14). The most recent incarnation of population genetics, known as coalescent theory, also incorporates variation in known gene sequences, and so includes data and concepts from levels extending from the genome to populations (Chapter 8). The models, though complex, make predictions about the sequence possessed by the most recent common ancestor of the population and how population numbers have varied since this organism lived. Coalescent theory captures a great amount of complexity and is a prime example of broad systems biology, although it is not usually viewed in this context.

Complexity is ubiquitous across evolutionary studies. Although the concept of descent with modification is straightforward in principle, it is not in practice. While the fitness of a variant in a given environment can sometimes be measured as a numerical constant, rarely, if ever, can that constant be calculated or predicted. This is because the extent to which one variant organism leaves more or fewer offspring in a particular environment than its peers depends on many factors, some of which may interact. It is premature to expect that systems biology can yet solve the difficult problems of the science of evolution, but, without some means of dealing with the intrinsic complexity of variation and selection, they will remain unsolved.

Nevertheless, and in spite of the fact that systems biology is a new and incomplete subject, it is to be hoped that its ideas will help illuminate some of the questions in evolutionary science that remain unanswered. A medieval rabbi remarked in a different context that “it is not your task to complete the work, but neither are you free to avoid it,” and so it is with evolution: every generation adds their perspective to a great tradition but there will always be further evolutionary problems to solve.

Further reading

Bard J (2013) Systems biology – the broader perspective. Cells 19:413–431.

Darwin C (1859) On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. http://darwin-online.org.uk/converted/pdf/1859_Origin_F373.pdf

Gilbert SF (2014) Developmental Biology, 10th ed. Sinauer Press.

Noble D (2008) The Music of Life: Biology Beyond Genes. Oxford University Press.

CHAPTER 2
A POTTED HISTORY OF EVOLUTIONARY SCIENCE

This chapter briefly summarizes the key steps and the major figures over the last 200 or so years who were responsible for the modern understanding of evolution. It provides the context for appreciating the many strands that make up our contemporary understanding of the subject. A much fuller history of this fascinating story, together with references, is given in Appendix 2.

The pre-Darwinian era

Until the end of the eighteenth century, the general belief across Europe was that the Bible provided a true account of the origins of life, although a few people had had their doubts. The first serious step that led the way to modern views of evolution came from Charles Bonnet, a Swiss biologist, who originally trained and practiced as a lawyer. Around 1770, he suggested that there had been progress up the great chain of being (or the ladder of life) from basal molds through plants, insects, worms, shellfish on to fish, birds, and quadrupeds to the ultimate perfection of man. Other naturalists such as Erasmus Darwin also put forward ideas that life had evolved from primitive origins, but all their arguments were based on logic rather than evidence.

There were actually quite good reasons for believing the Bible then: the biological world seemed constant and static, animals were perfectly suited to their environment, one species could not breed with another, and there was little or no evidence in favor of any other account. The Bible story was credible because there was no alternative rational explanation (albeit that the Bible gives different creation stories in Genesis 1 and 2). The one oddity was the presence of fossils, but these were mainly viewed as organisms either lost in or displaced by Noah’s flood.

The first evolutionary scientist in any modern sense was Jean-Baptiste Lamarck (1744–1829): he realized that, on the basis of tissue geometry, annelid and parasitic worms could not be treated as being on the same step of the ladder, as Bonnet had suggested: the anatomy of the former was far more complicated than that of the latter, and, in particular, had a coelom or body cavity. In 1809, he suggested that evolution occurred, not by ascending a ladder, but through successive descending branches from a common root. Lamarck was thus the first person to put forward the idea of descent with modification and did so on the basis of scientific evidence. He did not, of course, know how change happened or was inherited, but suggested that organisms...