All species on Earth share common ancestry – we are all part of the same family tree. The tree of life is a representation of how all those species are related to one another. All living species on Earth are the product of billions of years of evolution, so all are evolutionary equals in that way. However, we tend to think of life in a hierarchical way. We think there are lower animals and higher animals. We may incorrectly think that species of bacteria are old and primitive, and that humans are recent and advanced. Many news articles about evolution can feed into the perceptions that some species are younger, more advanced, or more evolved. But all of those perceptions are misleading. Each of these present-day species are our evolutionary cousins. All species alive today are the product of the same 3.5 billion years of evolutionary change, each adapting to their own environment. (Note that species are the units of evolution, frequently defined based on the distinctiveness of their appearance and genetics, and often on their ability to interbreed and produce fertile offspring.)
There are a number of causes of the misperception that there is some hierarchy of species. In particular, many people misread depictions of the tree of life, sometimes reading trees to indicate that some species are “more advanced” or “more evolved.” This furthers the misconception that life is a ladder of progress, and that humans are the definitive apex of that hierarchy. Thinking of life in these hierarchical ways is deeply engrained in our cultures, and likely traces back to religious beliefs, especially those related to the Great Chain of Being. It may be natural for humans to think of ourselves as the best and as the logical apex of evolution. However, human superiority is likely the most fundamental misconception about evolution and the history of life on Earth.
The goal of this book is understanding the tree of life. This book will: (1) explain how evolutionary tree diagrams depict the history of evolution; (2) help dispel misconceptions about evolution; and (3) use the tree of life to systematically explore the diversity of life on Earth. Understanding the Tree of Life addresses some of the most fundamental questions about life: Who are we, where did we come from, where do we fit in with the rest of life, and does that impact how we interact with our fellow organisms on this planet?
The Last Universal Common Ancestor and Growing the Tree of Life
Every single lineage alive today ultimately descended from a group of microorganisms that existed roughly 3.5 billion years ago. That we all trace back to an ancient common ancestor is profound. We refer to that ancestor as LUCA – the last universal common ancestor.
From LUCA, life began to diversify, and as evolution happened, the tree of life grew. A single lineage diversified into several lineages, and later tens of lineages, then hundreds, thousands, and eventually millions of species. The tree of life connects all those species. It can be depicted using diagrams illustrating how groups of species are related to one another. The tree of life is a concept that unites all life on Earth.
Charles Darwin realized that all organisms share common ancestry, and he was the first to conceive of a tree of life. In one of his notebooks, Darwin drew a simple branching diagram as he began to envision species diversifying. Above the drawing he wrote, cryptically and perhaps ambitiously: “I think” (Figure 1.1). Arguably this was one of the biggest thoughts, one of the most important ideas, of all time.
Darwin’s On the Origin of Species is undoubtedly one of the most important scientific works ever published. There is only one figure in the Origin of Species: It is a simple illustration of a few lineages, showing his idea of how lineages could divide and diversify over time. Clearly Darwin viewed the idea of common descent and the tree of life as central to understanding life on Earth.
How Does Evolution Happen?
Before we dive into the details of evolutionary trees, let’s think broadly about evolution, and how natural selection and species divergence happen. Darwin, along with Alfred Russell Wallace, came up with the concept of natural selection. We now know the details of how natural selection works. DNA carries information that leads to differences among organisms. (See Box 1.1 for a detailed explanation of DNA and evolution.) Individuals with some DNA variants (alleles) are more likely to survive and reproduce than others. Individuals with these favorable alleles survive and reproduce and thus pass those alleles on to their offspring. Those favored DNA variants increase in frequency, leading to changes in the genetic composition of the population over time. That is, in a nutshell, evolution by natural selection!
This book will speak a lot about evolutionary trees based on DNA data. Detailed information about molecular biology is beyond the scope of this book, but here is a quick overview of the aspects that are most relevant to understanding the tree of life.
All cellular organisms have DNA. Most human DNA occurs in our 46 chromosomes, including our two sex chromosomes – generally XX individuals identify as female and XY individuals identify as male. DNA has two strands, but we will focus on analyzing one strand at a time. DNA consists of building blocks called bases; the four bases are abbreviated A, T, C, and G (for adenine, thymine, cytosine, and guanine). Because there is always a T opposite an A and a G opposite a C, the two strands are complementary: If there is an ATCG sequence in one strand, there will be a TAGC sequence in the respective site of the other strand.
Many segments of DNA contain the information for cells to make proteins – in the lingo, these are genes that encode proteins. For example, there is a gene that encodes the enzyme lysozyme (which, among other things, attacks invading bacteria in our mouths or eyes). Imagine a six-base section of the human lysozyme gene with the following DNA sequence: TAC,AGG. In each of these protein-coding genes, the DNA bases are organized into three-letter groups that we call codons. Our cells “read” the information from the gene in our chromosomes, and ultimately that information is translated to build a protein – in this case, the enzyme lysozyme.
Proteins are made of strings of amino acids, and each codon code represents the code for a specific amino acid. You and I and most other organisms have a total of 20 different amino acids that are assembled in different ways to make a variety of proteins. When our cells read “TAC,” the amino acid tyrosine is added to the protein. When our cells read “AGG,” the amino acid arginine is added to the protein. Thus, you and I have the amino acids tyrosine and arginine in a key part of the lysozyme that is likely now in the tears of your eyes.
One of the scientists on my PhD thesis committee was Caro-Beth Stewart. As a PhD student at the University of California, Berkeley in the late 1980s, she used novel approaches to sequence DNA from the lysozyme gene of humans and five other primates and mammals. She showed that some primates (specifically leaf-eating monkeys) carried a new mutation that changed a key amino acid. The new mutation resulted in a slightly different version of lysozyme that helps digest bacteria in the guts of monkeys. We now know that in that segment of DNA, you and I have TAC,AGG, whereas leaf-eating langur monkeys have TAC,AAG. Just one mutation from G to A in that second three-letter codon changes the amino acid. For that key segment of the protein, you and I have the amino acids tyrosine and arginine, whereas the langur monkey has the amino acids tyrosine and lysine.
More generally, changes in the DNA of protein-coding genes lead to changes in amino acids, resulting in proteins with slightly different properties. In the case of the leaf-eating monkeys, natural selection led to the evolution of a different enzyme that enables them to digest the bacteria in their guts (which feed on the leaves they eat). Other examples could be a change in a gene related to melanin that would cause changes in skin or hair color in a mammal. A change in another gene might lead to depositing more calcium in a growing bone, causing changes in skeletal shape. Or a mutation in a gene involved in signaling between nerve cells might cause a change in behavior. Mutations in DNA produce new alleles, which may lead to changes in proteins, which may lead to changes in bones, digestive enzymes, behaviors, and more. Natural selection and random changes can increase or decrease the frequency of those alleles.
Hopi Hoekstra at Harvard University has documented exactly how natural selection played out in deer mice in the Sand Hills of Nebraska in the Midwestern US. A specific segment of DNA, a gene named agouti, influences coat color in the mice. The ancestral coat color was likely dark brown and the key segment of DNA that controls coat color had the sequence ATCAGC. However, a mutation occurred at the end of that segment – the C changed to a T. The ancestral allele was ATCAGC and the new allele was ATCAGT. This change led to a different amino acid in a protein, which led to a change in coat color. The lighter color pattern was less visible to predators against the light sand, so the light-colored individuals were more able to avoid predation than the dark-colored ones. More light-colored mice survived, so the new allele for light coloration increased in frequency (spread) in the population, and now light-colored mice predominate in the Sand Hills. Hoekstra and her collaborators demonstrated exactly how natural selection had acted. One DNA variant had spread through the population because it helped hide mice from predators – evolution by natural selection in action.
Mutations can also change in frequency due to random factors; for example, a pregnant mouse could fall in a river and end up on the other side, founding a new population. Whichever DNA variants that founder mouse carry will be more common in the new population. Similarly, if a tsunami wipes out 95 percent of the mice on an island, the few individuals that survive may happen to carry some alleles that were rare before. Such random changes in the frequency of different genetic variants – random fluctuations in allele frequencies – are known as genetic drift.
Mutations, natural selection, and genetic drift are occurring in all species at one level or another all the time – evolution happens. Individuals hatch, germinate, and are born every single day: some of these survive, some die in hurricanes; some reproduce a little, some reproduce a lot. All of this leads to changes in allele frequency over time – that is evolution. Formally and at its most basic, evolution is defined as a change in frequency of genetic variants over time. Although evolution is always occurring, it can be hard to fathom because these changes occur at such a slow rate that they are generally impossible for us to directly perceive.
How Do Lineages Diverge? Geographic Speciation
Darwin did a good job of explaining how evolution occurs within a lineage. We now know that mutation, selection, and drift can lead to major changes in coloration, physiology, behavior, and so on. However, Darwin did not really figure out how the number of lineages increases over time. Although the short title of Darwin’s book was On the Origin of Species, Darwin did not flesh out how two lineages can diverge. He did not actually explain speciation – the process of a single lineage diverging into two over time.
Ernst Mayr was an ornithologist who developed the concept of geographic speciation. He was studying birds in the South Pacific in the 1930s, and he noticed slight variations in coloration of bird species on different islands. Mayr realized that geographic isolation could be key in allowing different lineages to evolve along different pathways. His ideas of geographic speciation were a key addition to Darwin’s ideas. Mayr envisioned how a single parental species of bird could end up being isolated on two different islands, and thus over time diverge into two daughter species.
One of the main ways that geographic speciation occurs is that geological change splits a single ancestral species into two descendant species. I am going to call this speciation by geology (formally termed vicariance). For example, during the last glacial period, the grazing animals similar to today’s reindeer that lived in what is now Alaska and Siberia existed as a single population. Lower sea levels meant that the Bering Land Bridge allowed reindeer (Rangifer tarandus; referred to as caribou in North America) to freely move east and west. However, beginning around 20,000 years ago as the ice sheets melted, the sea level rose. By 10,000 years ago the land bridge was completely submerged. Thus, the reindeer on the east and west were cut off from each other. The longer these populations are isolated from each other, the more distinct they will become as they do not interbreed. Eventually, after tens of thousands or hundreds of thousands of years, they may become distinctive enough and/or evolve differences in reproductive behaviors so that scientists classify them as different species.
This geographic barrier was caused by a change in the landscape – a change in sea level due to geological change. Other such barriers could be caused by a mountain range forming, a canyon eroding, a river changing course, or an isthmus rising and separating two seas. In all these cases, the organisms do not move, but their ancestral populations are divided when the Earth’s surface changes.
Another example demonstrating speciation by geology involves the separation of two of our closest cousins. River formation likely caused the divergence of the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). Roughly two million years ago (mya), a single medium-sized ape was widespread in Central Africa. When the Congo River formed roughly 1.8 mya, it divided this “proto-Pan” population into two populations: (1) a northern population that evolved into today’s chimpanzee; and (2) a southern population that evolved into today’s bonobo. A new geological feature initially formed; then, during the next 1.8 million years, the two lineages evolved enough physical, genetic, and behavioral differences that biologists consider them clearly different species today.
Figure 1.2 can be used to illustrate any of the aforementioned scenarios. Imagine a single ancestral population of reindeer (A) moving freely back and forth across the Bering Land Bridge region. Then the ocean rises, creating a geographic barrier resulting in two separate landmasses and two separate reindeer populations (B in Siberia and C in Alaska and Canada). Over millions of years, two separate species are likely to have evolved.
Figure 1.2 Speciation occurs when a single lineage divides into two. On the left, there was a single ancestral species (A) present two million years ago. That single species was divided into two groups by a geographic barrier one million years ago. Now on the right, in the present day, there are two descendant species present (B and C).
Figure 1.2 has a time axis – the past is on the left and the present is on the right. Evolution is change over time, so most of the figures in this book will have this important time axis. Crucially, it is not really that “new species” are formed. Rather, a single ancestral species becomes spatially divided and eventually evolves into two descendant species. Mutations, natural selection, and genetic drift now simply happen in separated geographic locations. Evolution continues just like in other situations; however, now it occurs in two places separated by mountains, rivers, oceans, etc. If the geographic barrier is sufficient to prevent most individuals from crossing, over time enough differences will evolve in the two subpopulations that they will end up being considered different species – based on their appearance, behavior, and ability to interbreed. (Knowing exactly when to consider them different species can be challenging, and there are many different species definitions – these are explored in detail in another title in this series, Understanding Species by John Wilkens.) Other types of speciation are discussed in Box 1.2.
Another way that speciation can occur is when the organisms cross an existing geographic barrier – this is called speciation by dispersal; the geology does not change, but the organisms move. For example, the islands of the Bahamas have never been connected to Cuba or Florida by land. However, many plants and animals have colonized them. Many species of songbirds now inhabit the Bahamas, including one that I study known as the Bahama oriole. Orioles likely made it to the Bahamas by flying across the ocean, most likely from Cuba, where a close cousin species now lives – the Cuban oriole.
In this case the geology need not have changed at all. The birds crossed the geographic barrier; they moved via dispersal. Usually when this happens a small number of individuals found the new population, so speciation due to dispersal is often called founder event speciation. The birds on Cuba and the Bahamas are geographically separated by the ocean, they generally do not encounter each other, and they do not interbreed. Thus, they eventually became two distinct species. The birds in both the Bahamas and in Cuba continue to evolve.
Looking at Figure 1.2, imagine a single population of ancestral orioles on Cuba (A), perhaps colored black with moderate amounts of yellow. A few individuals are blown over from Cuba to the Bahamas, which results in two different lineages. Today we have two separate species – species B, the Bahama oriole with lots of yellow, and species C, the current-day Cuban oriole with very little yellow. (Note that the Cuban oriole would not be a living “ancestral oriole”; rather it likely just occupies the ancestral range.)
Finally, speciation can sometimes happen without a geographic barrier; these forms of speciation are less common and beyond the scope of this book. Also, this book will emphasize speciation resulting in two descendant lineages, leading to bifurcations in the tree of life. However, it is possible that a rise in sea level could simultaneously isolate organisms on three separate islands, leading to three equally closely related species of lizards, for example. This or similar cases would result in a trifurcation or trichotomy, which the book will not discuss further.
Speciation Continues, Life Diversifies, and the Tree of Life “Grows”
During the history of life on Earth, geological barriers and biological processes have subdivided lineages millions and millions of times. Although speciation can take thousands to millions of years, life has had roughly four billion years to diversify into all the species present today. The basic process shown in Figure 1.2 simply repeats itself over and over again.
Figure 1.3 is based on the same idea as Figure 1.2, but instead of one speciation event, we now see a total of three speciation events. The figure depicts a hypothetical lineage of mice evolving over the past four million years. Initially there was a widespread species of mouse (X). Three million years ago, the sea level rose and separated the ancestral mouse species into two geographic regions. Mutation, selection, and drift occurred, and new characteristics evolved in each of the two daughter species (Y and Z). Then, 2 mya, a chain of volcanoes formed, splitting the range of species Y in two. Mutation, selection, and drift continued in all three mouse lineages, and evolutionary changes accumulated. Finally, 1.5 mya, a river began forming a deep canyon that eventually split the range of species Z in two. Evolution continued, and today there are four species of mice (A–D). These are the present-day species, or extant species (the opposite of extinct). Figure 1.3 shows differences in the coloration of the mice. These differences signify the many differences that might have evolved in multiple aspects of these mice, including ecology, physiology, and mating behavior of the four species.
Figure 1.3 Detailed speciation scenario in mice, showing how a single ancestral mouse population diverges over four million years, leading to four present-day species: A, B, C, and D. Differences in the coloration of the mice – for example, in the body, ears, paws, and tail – signify the many differences that might have evolved in the four species.
What we see in Figure 1.3 is a detailed speciation scenario, including detailed illustrations of the mice and the geological events that caused the speciation. If one simply removes those illustrations, the remaining lines and arrows form a basic diagram representing the evolutionary history of this group. Because this diagram includes detailed information about time, it is called a chronogram (or timetree). A chronogram always includes a time axis labeled with the actual units of time, often in millions of years. This type of evolutionary tree is a scaled tree; in this case the tree is drawn to scale, with the length of the branches representing time.
Figure 1.3 also includes the most basic and the most important information about how these four species are related to one another. Specifically, species A and B are more closely related to each other than either is to species C or D. We know this because species A and B share a more recent common ancestor (Y) with each other than with the other two species. Species C and D are more closely related to each other than either is to A or B. One only has to go back 1.5 million years to find when C and D last shared a common ancestor. However, one has to go back three million years to find the common ancestor that C or D shares with A or B. Whenever considering evolutionary trees, more closely related means shares a more recent common ancestor. (In other words, the common ancestor lived closer to the present day.)
This terminology corresponds well to how we think about relatives in our families. I am more closely related to my brother than to my cousin. My brother and I share a parent, whereas one has to go further back in time to my grandfather to find the ancestor I share with my cousin. We share more recent ancestry with our siblings than we do with our first cousins. We have to go back yet another generation to a great-grandparent to find the most recent common ancestor we share with our second cousins.
Types of Evolutionary Diagrams: Chronograms and Cladograms Are Phylogenies
Take a look at Figure 1.4. Whereas it retains the key information from Figure 1.3 about relationships, it is not drawn to scale – it is an unscaled tree. Nevertheless, we can still see that species A and B are closely related, because we can still see that they share a common ancestor with each other more recently than the other two species. And here comes a crucial term – we say that species A and B form a clade. Species C and D form a second clade. A clade consists of all the species that share a more recent common ancestor with one another than with any other species on the tree.
Figure 1.4 Cladogram showing the relationships among the same four species of mice as Figure 1.3. However, details are removed, especially the exact timing of speciation events.
Figure 1.4Long description
A single ancestral species branches into two, each of which further splits, resulting in four species. Species A and B are closely related, as are species C and D. Species A has its body highlighted, B has its legs highlighted, C has its ears and tail highlighted, and D has no parts highlighted. All four species trace back to a common ancestor.
Unscaled trees that only show clades are known as cladograms. Note that all four species together– A, B, C, and D – also form a clade. Cladograms show relationships without exact timing; the lengths of the branches do not carry any information. Time is still represented in Figure 1.4, but not in an exact way. The past is still at the far left and the present is still at the far right, so in general time moves from left to right. But this figure does not include information as to exactly when the three speciation events happened. In contrast, chronograms/timetrees show the relationships along with the added information of a specific timescale.
Cladograms and chronograms are the two most commonly used types of evolutionary diagrams – they are two different types of phylogenies. A phylogeny can be defined simply as an evolutionary diagram showing relationships among organisms. The phylogeny of all life on Earth is the tree of life. Learning to interpret phylogenies – learning tree thinking – is key to understanding the tree of life and the evolution of life on Earth.
Figure 1.5 has the exact same information about relationships as Figure 1.4 – it is just drawn in a slightly different way. Figure 1.4 is a horizontal cladogram with rectangular branches, whereas Figure 1.5 is a vertical cladogram with slanted branches. At the top of the tree we see the tips of the branches. These are usually species, but they could also be whole groups of organisms, or at the other extreme individuals or even specific genes. In this book the species shown are generally sampled in the present day; in other words, this book focuses on extant species.
Figure 1.5 is labeled with key botanical terms that we use for phylogenies. We can refer to the species at the tips as leaves. The tree mostly consists of branches that connect the extant species with ancestral nodes. These nodes represent the speciation events that occurred in the past. The part of the tree furthest in the past is known as the root. The root represents the common ancestor that all species on the tree share. Going back to the mice, the root represents that ancestral mouse species that existed 3–4 mya. The root node (or basal node) represents the first speciation event in this group of organisms. All these botanical terms are key – leaves, branches, nodes, and a root. But there is one key botanical term missing from these trees.
There Is No Trunk in Twenty-First-Century Trees: There Is No Ladder of Progress
There is one plant part missing from present-day evolutionary trees – there is no trunk! A trunk would imply a main path to evolution. It would imply that evolution has a goal. A trunk would signify a main “direction” to evolution – for example, if there was a drive pushing most evolution toward large multicellular intelligent organisms. Understanding that there is no goal to evolution, that there is no single endpoint, is essential to understanding the entire process of evolution. Evolution has no aim, no target, no foresight.
However, 150 years ago, early biologists had not yet figured this out. In 1866, a German biologist named Ernst Haeckel published the first attempt to illustrate how all organisms are related to one another. He drew the first tree of life, and he in fact coined the term phylogeny for such trees. There are several key flaws with his depiction of the tree of life (Figure 1.6). First, Haeckel’s tree shows a prominent trunk, clearly suggesting a main path to evolution. Second, Haeckel’s tree shows a single species at the “top” of the tree of life, “man,” as if we were the goal or aim of evolution.
Figure 1.6 Ernst Haeckel’s depiction of the tree of life. Note that the most prominent part of his drawing is the trunk, and that there are four levels of a hierarchy of life in his drawing. Several extant groups are shown within the trunk, including bacteria (Monera), amoebas, worms, and amphibians. This depiction implies that these living groups are ancestral to other living groups, including man.
More generally, Haeckel’s tree shows a hierarchy of life: Some organisms are low down on the tree and others are higher up. He labeled four levels of hierarchy from bottom to top: “primitive animals,” then “invertebrates,” then “vertebrates,” then “mammals.” His depiction traces back to Aristotle’s scala naturae, which showed the natural world as being organized into lower and higher forms. Thus, Haeckel’s tree shows a ladder of progress, implying that life began with “primitive” organisms, then advanced to “higher” forms, culminating in man. Bacteria and amoeba are shown at the bottom in the trunk, followed by snails and worms, followed by fishes and amphibians, and on to the mammals at the top. Within the mammals, “primitive mammals” and pouched mammals are shown at the bottom, followed by lemurs, then apes, then humans at the very top.
The idea of humans being the most advanced form of life is central to many misconceptions about how evolution occurs and about where we fit in with the rest of life. Although evolutionary biologists are making headway dispelling these centuries-old notions of a hierarchy of life, there are still many biologists that speak, for example, of “lower plants” and “higher plants,” or “advanced vertebrates” and “primitive mammals” (later chapters will address specific examples). It is very difficult to step back and try to have an objective view of life, and it is quite understandable that we might incorrectly think of ourselves as being exceptional, advanced, or superior.
In fact, it is quite understandable for humans to think of ourselves as the center of the universe. Many creation myths begin with one specific tribe being placed in the center of the Earth. Aristotle drew a view of the universe that showed Earth at the center. As astronomy matured, it became clear that everything did not revolve around the Earth, and Copernicus developed a view of the universe with the Sun at the center. Galileo observed the orbit of moons around Jupiter and thus showed that the Earth-as-center view was incorrect. One might be tempted to think that we might at least be at the center of our galaxy, but our Sun is off to the side, between two major arms of the Milky Way. Perhaps the Milky Way is at least near the center of the universe? Astronomers have now concluded that there is no center of the universe!
In a similar way, over the last two centuries, biologists have slowly realized that across extant species there is no center of the tree of life. As mentioned, centuries ago, many creation myths put humans at the center of creation. Then Haeckel drew a tree of life that acknowledged evolution, but still put humans at the center, at the top of the tree of life. Now, over 150 years later, biologists are finally realizing that there is no single top of the tree of life, and old notions of higher and lower organisms are fundamentally flawed. Tackling a wide range of challenges in science, social science, and public policy will be hampered if we begin from a flawed hierarchical view of the tree of life.
Today’s phylogenies generally show all extant species lined up in the present (e.g., Figure 1.5). There is no single top to the tree of life; each of the millions of extant species represents the most recent products of evolution. Misunderstanding our place among our fellow species, and misunderstanding our place in the universe, could be a recipe for disaster. Stated simply, if we do not know where we are and how we got here, we are bound to get lost. Nothing is more important for our concept of who we are and where we are going. We are not at the center of the universe – neither in space nor conceptually – and we are not the one inevitable product of some kind of goal-directed evolution. There is no center of the universe and there is no hierarchy of life. Understanding our place in the universe and understanding the tree of life are crucial to thinking about how we as a species move forward.
This Tale Starts with Humans: Cousin Trees
As just discussed, a fundamental misconception about evolution and the tree of life is that evolution has a goal and that humans represent the ultimate endpoint of evolution. Textbooks used in secondary school and university biology courses survey the diversity of life, describing key aspects of groups of organisms across the full diversity of life on Earth. Almost all such textbooks start with bacteria and end with humans, an approach that may give the impression that there is progression leading in the end to humans. For example, the excellent text that I teach from starts with bacteria, then goes through plants, fungi, and invertebrate animals, before ending with fishes, reptiles, and finally with humans. The last two pages from that text focus on the recent history of Homo sapiens, where we originated from and how we spread across the planet. This march across the diversity of life ending with humans can certainly lead to the misconception that we are the endpoint of evolution. It is as if each succeeding chapter represents some addition of yet more “advanced” characteristics, all of which leads to humans.
To avoid this misconception, this book starts with humans. Not because humans are special in some grand sense. Not because we are the most advanced species. Not because we are the most recent product of evolution. None of those are true. I start with humans simply because we are humans – the readers of this book are Homo sapiens. If the readers were sea urchins, or pine trees, or mushrooms, the book could start with them. Richard Dawkins’ book The Ancestor’s Tale also starts with humans for a similar reason, and works back in time focusing on the ancestors that unite us.
However, the focus of the current book is on cousins and on using extant species to help understand the tree of life – how to read evolutionary trees of today’s species in a way that avoids misconceptions. Starting with humans and working out to more and more distant relatives helps us realize that humans are one of the millions of species at the tips of the branches all across the tree of life. Figure 1.7 shows one simple tree of life with nine species that represent nine groups of the tree of life – nine living species at the tips of the branches. Note that most trees in this book will not have humans at the top or the far right.
Figure 1.7 An evolutionary tree showing humans and eight of our cousin lineages. This tree is drawn with a human focus, so it might make it look like humans are at the “top” of the evolutionary tree, but this book will explain why that perception is incorrect. This tree spans all the chapters of this book. This tree simply says humans are more closely related to chimpanzees than we are to platypuses. It also says that the three mammals are one another’s closest relatives on the tree. Birds are more closely related to us than frogs are, and salmon have a more recent common ancestor with us than they do with sponges. Finally, fungi group with animals to the exclusion of bacteria. As with most trees in this book, the time axis moves from left to right – past to present. Be careful not to think that bacteria are the furthest in the past and that humans are in the present. The axis from bottom to top – the axis opposite to time – generally means nothing! To reiterate, reading from bottom to top might make one think that evolution started with bacteria and then life increased in “complexity,” eventually leading to humans – that reading is incorrect, as this book will demonstrate.
Each chapter of the book will focus on more and more distant cousins: We start with humans, then chimpanzees and other primates, then other mammals and so on, all the way to our most distant cousins – bacteria. Figure 1.7 is a very basic tree of life, with one representative organism from each subsequent chapter. Chapter 2 discusses human evolution, and demonstrates how closely related we all are to one another. Chapter 3 shows how we are related to other primates and explains that chimpanzees are not our ancestors. Chapter 4 addresses how we fit in with other mammals, and I argue that it is misleading to think of the egg-laying platypus as “primitive.” Chapter 5 focuses on reptiles and explains that birds are reptiles! Chapter 6 explains that we are tetrapods, along with reptiles, frogs, and other amphibians. Chapter 7 is about “fishes” and demonstrates that fish are not a true evolutionary group, and that salmon are more closely related to us than they are to sharks. Chapter 8 shows where we fit in with other animals, and details how we did not evolve from living groups such as sponges. Chapter 9 shows how we are related to other multicellular groups of organisms – surprisingly, fungi are more closely related to animals than they are to plants. Finally, Chapter 10 explains that Bacteria are our most distant cousins, and that we did not evolve from Bacteria.
Avoiding Misconceptions about Evolution and the Tree of Life
Each chapter also deals with some of the major misconceptions about how evolutionary trees are read. There are few areas of biology and evolution burdened by so many misunderstandings. These misconceptions have several causes. There are misconceptions based on how our minds interpret evolutionary trees, misconceptions based on cultural biases, misconceptions promulgated in the popular press, and even misconceptions taught by accomplished biologists who do not focus on phylogenies. These misconceptions make it hard to understand what evolutionary trees can really tell us about evolution. Table 1.1 lists some of these and the main chapters that address these misconceptions. This book will illustrate at all levels of the tree of life how these misconceptions have pervaded our understanding of evolution and clouded our understanding of life on Earth.
To reiterate what is at stake, misconceptions about the tree of life lead to misconceptions about how evolution happens, which lead to misconceptions about all life. The main goal of this book is to address those misconceptions. Misunderstanding the tree of life leads to misunderstanding the entire history of life on Earth.
On the other hand, more clear understanding of evolutionary trees and the process of evolution can lead to exciting insights into how life unfolded on this planet over the last four billion years. The most important message of the whole book is that all humans, all animals, all living species are evolutionary cousins of one another. Understanding phylogenetic trees is central to understanding life itself: how we got here and how we think about our future.
My objective is to enable readers to understand how all life on Earth is related. Importantly, I will focus on individuals and species sampled in the present day – there will not be much discussion of fossils, geology, and extinct lineages. The book is about the phylogeny that connects Homo sapiens with all other living species on the planet – in other words, I will de-emphasize extinct species and emphasize extant species. Extant species are all one another’s cousins – cousins have “lateral” relationships, not “vertical” ancestor–descendant relationships. This book is a cousin’s tale – the story of how you and I are related to all life on Earth.
Evolution is the foundation for understanding all of biology. The well-known twentieth-century biologist Theodosius Dobzhansky famously wrote: “Nothing in biology makes sense except in the light of evolution.” An extension of this points out that nothing in evolution makes sense except in the light of phylogeny. Understanding the tree of life is fundamental to how we conceive of our connection to all life on Earth and ultimately central to how we view our place in the universe!
Organisms that were perceived to be simpler such as plants, sponges and worms were placed lower on the ladder, and organisms like lizards, dogs and humans were perched higher in accordance with the sense that they are more complex and thus “superior.” We now understand that any such ranking of living species is invalid.
