Evolution's New Narrative

Life is a decentralized, horizontal network, not merely a centralized, hierarchical tree.

The conventional narrative for evolution is outdated. I am not casting doubt on the fact of evolution. I am saying that the way most people think of life's story has not kept pace with new knowledge about evolution's many and disparate paths.

The short version of the conventional narrative describes life as one big family linked by common ancestry. All of us, from bacteria to kelp, condors, and people, are fellow travelers through time, sharing our deepest and oldest roots. In this narrative, the path of common ancestry is a sprawling series of splitting events. A single species splits to become two, and those two species become four, which become eight, then 16, then 32, and so on, with bifurcating branches for millions of species. In this view, the course of common ancestry is diagrammed as a tree, with dividing branches denoting species, and is linked to the process of natural selection, which favors those individuals and groups enjoying greater reproductive success. As Charles Darwin wrote: "The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth."

The change in evolution's narrative that I advance here emphasizes the sharing of genetic materials among different species, and a greater role for the influence of species on their mutual genetic change. I use "horizontal evolution" as a broad umbrella term to cover the various processes for this genetic integration among life forms.

In vertical evolution, genetic material passes from parents to progeny. By contrast, horizontal evolution often entails transfer of genes that is not from parents to progeny. Most of us don't know much of the copious evidence coming to light for horizontal evolution, even within our own past: It is buried in our genomes, a result of events ranging from ancient horizontal gene transfers from viruses to relatively recent hybridization among different species of Homo. The bias of our experience makes it easy to miss the radical plot twists that horizontal evolution knits into the narrative of change.

By taking both horizontal and vertical evolution into account, we can understand the phylogeny for all of life, the overall pattern of genealogy, as a network. This network resembles the tree familiar to us from the conventional model of evolution, but it adds horizontal connections among branches, as species alternately diverge and integrate.

How Evolution's Narrative Evolved

Ötzi, also known as the Tyrolean Iceman, was born about 5,300 years ago and died, apparently murdered, at the age of 45. With graying brown hair and a thin beard, his five-foot-four-inch, 110-pound body lay frozen and well-preserved in a glacier for millennia. He was spotted by hikers in 1991 high in the mountains along the Italian and Austrian border, as his icy crypt melted.

We're ignorant of Ötzi's views on life's history, but he had an expert's knowledge of nature by necessity. To judge from his possessions and clothing, he was ingeniously equipped for survival, stemming from his cultural inheritance, his native intelligence, and millions of years of natural selection. His leggings were made from goat hides, and his coats and a loincloth were sheepskin patches stitched together with twisted tendon strips. His cap was a fitted piece of brown bear hide worn hair-side out. His shoes, nearly waterproof, had roe deer upper parts, soles made from brown bear hide, and laces from cattle hide. He carried a lightweight net for trapping small animals made from the pliable, strong inner bark fibers, called bast, from several different tree species. Ötzi carried masses of dried birch polypore fungus, Piptoporus betulina, on two narrow leather laces. When eaten, this fungus induces diarrhea and has some antibiotic and anti-inflammatory properties. No doubt, Ötzi attributed some benefit to the fungi he carried, and he may have been self-medicating with these as a treatment for his heavy whipworm infection.

Ötzi and his contemporaries were skilled in propagating domesticated plants and animals, carrying on the agricultural revolution that began about 12,500 years ago. They selected individual plants and animals for future breeding based on their traits and vigor. Often called artificial selection, this is actually natural selection in human hands.

Let's move ahead about 3,000 years to 340 BCE and consider the Greek naturalist and polymath Aristotle. Most of Aristotle's writing appears as informal notes, though scholars estimate those represent just 20 percent of his actual writings, the rest being lost. Aristotle's pioneering efforts, despite errors and inclusion of some folktales and nonscience, set a high standard. So high, nothing of comparable insight and scope appeared for more than 1,000 years.

Aristotle's work centered on direct observation in the wild and dissection of animals. He dissected at least 110 different species, including bats, octopi, dolphins, and chameleons. He used the wealth of facts gained in these detailed dissections and comparisons to better understand the distinctive kinds of life, their forms, and their functions. Aristotle's years of study led him to see similarities and a gradation in the differences among species, or forms, of organisms. He thought living and nonliving entities could be ordered along a scale of vitality, mobility, and, for some species, a potential based on development. He wrote: "Nature proceeds little by little from things lifeless to animal life in such a way that it is impossible to determine the exact line of demarcation….[A]fter lifeless things in the upward scale comes the plant, of which one will differ from another as to its amount of apparent vitality;…there is observed in plants a continuous scale of ascent towards the animal….[T]hroughout the entire animal scale there is a graduated differentiation in amount of vitality and in capacity for motion."

Aristotle's concept of a scale for life is simultaneously vague and bold. There is no metric for the scale; there are no units for degrees of vitality or mobility. But the idea of relating all life forms, as variants along a common thread, was new. It also broke with the prior classification methods that his contemporaries used outside of biology, on topics of mathematics, astronomy, and philosophy.

Aristotle mentioned names of about 230 different animals in his writings. Although he didn't explicitly assign them all to positions on a scale, we can depict his vision by putting some species into a rough sequence, starting with what he considered the "plant-like" invertebrate animals and continuing from there. Not in a straight line, but zigzagging, sometimes wildly, and tracing an arc of generalized progression in complexity and organization. We can begin with sea anemones and sponges, and move successively to hard-shelled animals with limpets and mussels, soft-shelled animals with crabs and lobster, soft-bodied animals with cuttlefish and octopus, insects with ants and butterflies, fishes with gobies and parrotfish, snakes with water snakes and vipers, egg-laying tetrapods with tortoises and chameleons, birds with bee-eaters and ravens, and mammals with otters and humans.

Aristotle's rough scale for natural entities, from minerals to plants and then animals, eventually gave rise to the idea of the scala naturae, or great chain of being, which became the dominant organizing concept for understanding living diversity for nearly two millennia. The scala naturae was often considered as arranging species in sequence of increasing perfection or complexity, with the humans at the top of the animal scale, and just below deity, although extending the scale of the scala naturae to heaven was not at all what Aristotle had in mind: Aristotle was committed to explaining the natural world based on natural causes, without invoking the supernatural. This commitment was not held by all who followed him.

We now jump ahead to the 18th-century botanist Carl Linnaeus. Like Aristotle, Linnaeus wanted to describe and organize all known life forms. He championed the use of binomials in taxonomy, consisting of genus and species names. Homo sapiens in our case.

Before Linnaeus, species names were jargon-filled strings of description trying to be diagnostic. For example, the Latin plant species name Plantago foliis ovato-lanceolatis pubescentibus, spica cylindrica, scapo tereti (in English: "plantain with pubescent ovate-lanceolate leaves, a cylindrical spike, and a terete scape") became simply Plantago media in Linnaeus's treatment. He understood that names couldn't function as species identification guides, given the pace of new species' discovery.

From 1735 to 1766, Linnaeus' book Systema Naturae went through 12 editions, in which he classified about 9,000 species of plants and 4,400 species of animals. What had been a slim volume of 12 pages became a three-volume series of 2,400 pages. Modern taxonomies still begin with his writings, and the idea of ranked categories of classes, orders, and genera is still in broad use, though not without controversy.

At the time, the dominant narrative for explaining life's diversity was biblical creation by God, and the number of species and their forms did not change. Though Linnaeus was a creationist, his astute observations of variation within and among species led him in his later years to doubt this view. He had witnessed the origins of new plant species via hybridization (different species interbreeding) in his extensive garden experiments. He and his students saw many wild plants intermediate in form between known species and considered them to be new species of hybrid origin. The 12th edition of Systema Naturae omitted a claim that Linnaeus had made in earlier editions: that new species do not form. This implicitly allowed the possibility of natural processes leading to the origin of new species. So although he was a creationist, he understood that some new species had arisen, naturally, since the creation.

Next in this selective review of evolution's changing narrative is the work of Charles Darwin, born 31 years after Linnaeus died. Darwin is well known as the founding father of evolutionary biology. Though he is less well known, the British naturalist Alfred Russel Wallace, who studied and developed his ideas independently from Darwin, was a co-discoverer of natural selection. Both linked the concept and process of natural selection to change in organisms over time, providing the key mechanism to the modern view of life's evolution. Wallace even expressed a similar view to Darwin's branching tree, describing relationships among species as involving "branching of the lines of affinity, as intricate as the twigs of a gnarled oak." Though they did publish together in 1858, Darwin's notebooks of 1837 show he had been developing the core ideas 21 years earlier. Darwin framed human evolution as another instance of material process and change. Wallace, however, held that human beings owed much of their mental and spiritual faculties to "an unseen universe—a world of Spirit…to which the world of matter is altogether subordinate," rather than natural selection.

The cultural impact of Darwin's narrative for human origins—the idea that all life, including us, shares common ancestry—was immediate, striking at the heart of nonscientific narratives. Though controversy continues in some circles, the fact of common ancestry for all life hasn't been a scientific controversy since Darwin's time.

This does not mean our knowledge is complete. Far from it. Many aspects of life's evolution remain to be discovered or reconsidered and integrated into our growing knowledge.

Evolutionists through the mid-20th century predominantly studied animals, and to a lesser degree plants, and the processes they discovered were placed front and center in evolution's overarching narrative. The conventional narrative has long emphasized that new species arise by branching off from others. This was a foundational insight from Darwin: early examples of speciation as a branching process, with one species splitting into two or, in cases of a species radiation, more than two, include the mockingbirds and finches that he studied on the Galápagos Islands.

A limiting aspect of the conventional evolutionary narrative is its inherent centralized view, which is baked into those branching tree diagrams. In that approach, each new species receives all its genes, and all the features they encode, from a single parental species—one centralized source.

Evolution's new narrative depicts a more decentralized network, where branches can both split and join. Or, better: Life is envisioned as a vast, tangled system of streams, variously dividing, joining, meandering, and dividing again.

In the past, some have sought to summarize evolution as a two-step process: first mutation, then natural selection favoring beneficial mutations. These remain key features, but an even broader pair of processes, in keeping with the new narrative for evolution, is that of divergence and integration, with mutation and selection operating within both.

The need for this new narrative stems not from any single recent discovery or eureka moment, but from the cumulative weight and synthesis of many discoveries about the functions and evolution of biological diversity, some dating back to the 19th century and many others based on current science. In recent years, there have been increasing calls for change from the conventional view, given these new discoveries. The evolutionary and molecular biologist W. Ford Doolittle was early to spotlight the problem: "If chimerism or lateral gene transfer cannot be dismissed as trivial in extent or limited to special categories of genes, then the history of life cannot properly be represented as a tree."

The Means of Horizontal Evolution

Horizontal evolution occurs along a continuum. This ranges from direct sharing of genetic material among different species, at the more material end, to mutual genetic influences among species, known as coevolution by natural selection, at the less material end. The three primary means of direct sharing are: (1) hybridization among sexual species and recombination among microbes, (2) the joining or merger of species, and (3) horizontal gene transfer.

Hybridization occurs when individuals of different sexually reproducing species interbreed. This leads to mixing of genes between the species, known as introgression. In recent years, the study of large genomic datasets has shown that introgression is much more common than previously thought. Domestic crops offer a clear example of hybridization in action. Many modern cultivars are the result of intentional hybridization followed by selection for variations in such features as taste, cold-hardiness, and disease resistance.

The joining or merger of species begins as interactions, including symbioses, among individuals from different species that become obligate and genetically integrated over time. A primary mechanism for joining species lineages is endosymbiosis: when one symbiont resides inside another. Some of the most consequential innovations in life's 3.8-billion-year history stem from a joining of previously distinct lineages by endosymbioses. This includes the origins of two essential components of cells: mitochondria (found in all animals, plants, and fungi) and chloroplasts (found in plants).

The third process is horizontal gene transfer. This is the movement of genetic material between organisms, outside of its vertical transfer between parents and progeny. Discoveries of horizontal gene transfer over the past 50 years have provided some of the biggest recent changes in our understanding of evolution, and it is now recognized as a dominant mode of evolution among microbes. Most, if not all, genes in the genomes of all bacteria and archaea (the oldest and most inclusive groups of single-celled life) have experienced horizontal gene transfer in their past. Horizontal gene transfer is comparatively rare in plants, fungi, and animals, but it is being discovered in them with increasing frequency. Given that early lineages of all multicellular life forms arose with the help of horizontal gene transfer among bacteria and archaea, horizontal gene transfer ranks as a key feature in life's evolution and an important part of the new narrative.

These three processes decentralize the material of inheritance. Decentralization is a key tenet of the new narrative of evolution: Many species can and do get their genes from one or more different species. This differs from the conventional view, in which a new species derives its genetic material from one, central parental species.

Horizontal evolution's strong decentralizing forces, both past and present, are much more than a trivial detail. Its pattern is opposite and complementary to that of conventional branching. Its consequences within the narrative are at least twofold: It can catalyze change within species as well as a dramatic proliferation of species. Horizontal evolution does not subsume the conventional narrative, but it shows the old story to be inadequate.

The fourth process under the umbrella of horizontal evolution is coevolution of species by natural selection. This happens over time between flowers and their pollinators, between predators and their prey, and between pathogens and their hosts, among other examples. Thus, deeper flower nectaries select for longer bills in hummingbirds, and greater virulence in pathogens selects for greater resistance in their hosts. By definition, coevolution yields heritable, genetic change among species over time, similar in the long run to the direct mechanisms of genetic sharing noted above. All species are subject to coevolution to some degree, but its impact in driving life's evolution is often underappreciated.

A Richer Map

As we internalize the new narrative, we can overcome many popular misconceptions about evolution and phylogeny. Here's a sampling:

Misconception: Phylogenetic trees and rooted networks show evolutionary progress, usually advancing from species on the left to those on the right.

Better conception: The ordering of tips has no meaning regarding progress; all tips denoting extant species are of equal age relative to shared common ancestors.

Misconception: Species arise by splitting only, with one becoming two.

Better conception: Species can also merge, with two becoming one.

Misconception: Some living species are ancestors of other living species.

Better conception: Living species are cousins, not ancestors.

Misconception: Species are consistently, clearly defined.

Better conception: In many cases, designating species is difficult.

Misconception: Evolution progresses from primitive forms to advanced.

Better conception: Evolution can yield both increased and decreased complexity.

Misconception: We've discovered most or all of Earth's unique life forms.

Better conception: The rate of discovery of new life forms and variants is as high as ever, in large part because of molecular sequencing efforts.

Misconception: Viruses are not alive.

Better conception: Viruses reproduce, carry genetic instructions, and evolve, and many biologists do consider viruses alive or in a gray zone.

Misconception: Inheritance of acquired features doesn't exist.

Better conception: Inheritance of acquired features is integral to horizontal evolution and, to a lesser degree, immune system evolution.

Misconception: All organisms, including human beings, are intelligently designed.

Better conception: Organisms change over time by processes of evolution and often include inefficient features.

Vertical evolution and conventional branching patterns remain key to the new narrative, especially among animals, but they are woefully insufficient to explain the entire genealogical network of life. Seeing diagrams of both vertical and horizontal evolution together is like gazing at a world map on a school classroom wall with the country and state borders clearly drawn, and then superimposing another map showing the highways and the airplane, train, and ferry routes that cross the borders and seas. This is a richer, more connected map.

David P. Mindell is a senior researcher at the Museum of Vertebrate Zoology at the University of California, Berkeley. His most recent book is The Network of Life: A New View of Evolution, from which this article is adapted with permission of Princeton University Press.