Phylogenetics and the History of Life
David A. Baum
As laid out by Charles Darwin, evolutionary theory is built around two key postulates (see Section I: Introduction). First, features of living species were acquired over time by evolution along lineages that have branched to form the evolutionary tree of life. Second, the good fit between organisms and their current way of life is explained by natural selection (and variants such as sexual and group selection). Although evolutionary biology has grown significantly in the century and a half since the publication of On the Origin of Species, these two points still constitute the central canon of evolutionary biology. They are overwhelmingly supported by empirical data, and are both essential aspects of biological literacy. Mechanisms of evolution, including natural selection, will be covered in the remaining sections of the book. In this section, however, we focus specifically on common ancestry and evolutionary trees, the first of Darwin’s postulates.
To motivate this section, and explain why it is placed so early in the book, consider the importance of common ancestry in the historical development of evolutionary theory. During his voyage on HMS Beagle, Charles Darwin was struck by changes in the living and fossil organisms he encountered in different parts of the world. These observations, combined with his already excellent knowledge of biological diversity, led him to “see” the pattern of evolutionary descent. He observed numerous patterns that would not be expected under the hypothesis of special creation, but could be explained readily if different species share descent from common ancestors (see chapter I.2). The discovery of common ancestry, with its implication that abundant evolution has happened, posed the question, What mechanism could explain such evolution while leading to a fit between organisms and their ways of life? This puzzle occupied Darwin for much of his scientific career, during which he also amassed further evidence for descent from common ancestry. However, it is fair to say that Darwin would have had no reason to begin his studies of pigeons, or to experiment on seed dispersal, and so on, if he had not first discovered the historical fact of evolution. In a book presenting our current understanding of evolutionary biology, it seems fitting, therefore, to begin by covering common ancestry and the history of life on earth, with subsequent chapters dealing with processes of evolution.
The first nine chapters in this section examine the methods by which scientists reconstruct and make sense of evolutionary history, whereas the last nine summarize what we now know about the evolutionary history of different parts of the tree of life.
A recurring motif throughout the chapters in this section is the study of phylogeny. Phylogenies are formal representations of Darwin’s metaphorical tree of life. Chapter II.1 introduces phylogenies and how to interpret them. This is important, because for all their utility in evolutionary biology, phylogenetic trees are notoriously easy to misunderstand. This chapter introduces phylogenetic terminology and explains what information can and cannot be extracted from a tree diagram.
chapters II.2 and II.3 introduce the methods used by scientists to obtain phylogenetic trees. The first of these chapters provides an overview of methods that aim to determine the correct tree topology, the ordering of lineage branching. It focuses on phylogenetic inference based on DNA sequence data, far and away the most widely used data source, and introduces the rigorous statistical methods that are now de rigueur in the field. Chapter II.4 extends this discussion yet further, focusing on the challenge of combining information from molecular data with that from geology or paleontology to infer the dates of branch points within a phylogeny. Such time-calibrated trees are especially useful for studies of the migration of lineages around the globe and those aiming to quantify the rates at which different lineages have diversified.
chapters II.4–II.7 are concerned with inferences about evolutionary history that can be made once phylogenetic trees have been determined. Chapter II.4 deals with historical biogeography, which entails using phylogenetic information to study the mechanisms (e.g., range expansion, range contraction, or long-distance dispersal) by which taxonomic groups came to have their current geographical distributions. The chapter provides an overview of the history of biogeography, a summary of some well-established biogeographic phenomena, and perspectives on controversies and future directions. Chapter II.5 follows nicely by considering phylogeography, a field that merges some aspects of biogeography with insights from population genetics (discussed in Section III: Natural Selection and Adaptation, and Section IV: Evolutionary Processes) to understand the spatial distribution of genetic variation within and among populations. Phylogeography is especially effective at studying recent migration patterns and patterns of gene flow among contemporary populations.
chapters II.6 and II.7 take two different perspectives on the study of character evolution in the context of phylogenetic information. Chapter II.6 focuses on statistical analyses that can be used to reconstruct ancestral states or to study the dynamics of trait evolution. Such statistical tests are important for, among other things, determining whether pairs of traits show correlated evolution or whether certain traits have altered the rate of speciation and extinction. Chapter II.7 takes a more conceptual approach, clarifying the macroevolutionary patterns that may be seen when looking across phylogenetic trees and providing a guide to the terminology used by biologists to describe these patterns, including such important terms as adaptation and homology.
Chapter II.8 considers another use of phylogenies: for organizing knowledge of diversity in the form of a taxonomy. The chapter charts the historical shift from taxonomy as a system for capturing the mind of the Creator to taxonomy as a reflection of evolutionary history. It also provides an introduction to phylogenetic nomenclature, an approach to connecting names to biological taxa, and explores some of the recent controversy this approach has engendered.
The aforementioned chapters in the section focus on the effort to make historical inferences by studying living organisms, largely overlooking paleontology (with the exception of some mentions of fossils in the context of molecular dating and historical biogeography). Chapter II.9, therefore, summarizes what can be learned by careful and critical analysis of the fossil record. These insights into paleontological methods and the geological time line provide the last critical pieces of information needed to delve into the actual history of life on earth, as outlined in chapters II.10–II.18.
The nine chapters on evolution of life on earth cover many of the most remarkable evolutionary transitions and describe the history of several of the most familiar and successful groups of living organisms. These chapters begin with the origin of life (see chapter II.10) and end with the origin of humans (see chapter II.18); however, this ordering should not be taken as endorsing the misguided view that humans are inherently more advanced than other living groups. While we are telling the story from the vantage point of humans by exploring events and groups in order of decreasing phylogenetic distance from the human lineage, this telling is not evolutionarily privileged. We could equally validly reorder the narrative around a particular group of bacteria, or plants, or snails, or whatever. That we did not do this reflects our sense that humans naturally tend toward linear stories, and furthermore stories that end at things they consider most important, in this case, humans themselves.
The first chapter in the section, chapter II.10, reviews current knowledge of the origin of life. While there is no consensus view, we now know a lot about the context and timing of life’s emergence, and increasingly sophisticated and compelling chemical models have been developed over the last couple of decades.
Chapter II.11 examines the prokaryotic grade, composed of bacteria and archaea, and explores their mode of evolution, including their propensity for lateral gene transfer. Often underemphasized because of their diminutive size, prokaryotic organisms play diverse, important ecological roles and encompass tremendous biochemical diversity. Similar themes emerge in chapter II.12, which examines the origin of eukaryotes and diversification of protists, which is to say eukaryotes that are not animals, fungi, or plants. The remarkable diversity and ecological significance of protists deserves much greater attention than is typical in biological education.
Chapter II.13 explores the origin and diversity of land plants. The invasion of land by green plants was a momentous event in the history of life on earth, eclipsed only by the origin of oxygenic photosynthesis in cyanobacteria (which established an oxygen-rich atmosphere). The radiation of land plants not only permitted the subsequent diversification of animals on land but also allowed for the evolution of diverse interactions with animals and fungi, including those involved in pollination and dispersal. Similarly, fungi, covered in chapter II.14, have played an important role in terrestrial life, especially as decomposers and through biotic interactions, ranging from pathogenic to mutualistic, such as root associations called mycorrhizae. Fungal phylogeny is now well understood, including the insight that fungi are closely related to animals, but there is evidence that much of fungal diversity remains to be characterized.
Chapters II.15–II.18 all deal with animals, the most apparent of the major branches of the tree of life. Chapter II.15 sets the stage by exploring the origin of animals from single-celled ancestors and the broad sweep of their diversification into major lineages. A central focus is on the dramatic, yet incomplete, progress that has been made in resolving relationships among the major animal groups.
Chapters II.16 and II.17 delve into two major clades (i.e., evolutionary lineages) that have been particularly successful and influential. Arthropods are numerically the most diverse animal phylum, including as they do arachnids, crustaceans, and above all, insects, yet until quite recently there was great uncertainty as to relationships among its major subgroups. As shown in chapter II.17, this contrasts with the situation with tetrapods, whose evolutionary history has been well understood for some time thanks to a rich fossil record and abundant, careful morphological work. Nonetheless, even in tetrapods, modern molecular data have been influential in shaping our understanding of the connection between different lineages and the mechanisms by which certain interesting traits evolved. Finally, chapter II.18 lays out the current state of play in the dynamic field of human evolution, showing how assorted lines of evidence, especially paleoanthropology and genomics, are converging to provide an ever richer and more complete understanding of how evolution came to yield a species that would develop the intellectual capacity to ponder its own evolutionary origin.
The diversity chapters in this section certainly fall far short of communicating all that we now know about the history of life on earth; nonetheless, taken together, they powerfully show how the use of methods described in the first half of the section can help us gain solid insights into the origins of the remarkable diversity of living organism that have existed and do exist on this planet.