What is evolutionary biology?

An Evolutionary Context

Life is self-perpetuating, with each generation connected to previous ones by the thread of DNA passed from ancestors to descendants. Life on Earth thus has a single history much like the genealogy of an extended family, the shape and characteristics of which have been determined by internal and external forces. The effort to uncover that history and describe the forces that shape it constitutes the field of evolutionary biology.

As an example of the need for this perspective, consider three vertebrates of different species, two aquatic (a whale and a fish) and one terrestrial (a deer). The two aquatic species share a torpedolike shape and oarlike appendages. These two species differ, however, in that one lays eggs and obtains oxygen from the water using gills, while the other produces live young and must breathe air at the surface. The terrestrial species has a different, less streamlined, shape and appendages for walking, but it too breathes air using lungs and produces live young. All three species are the same in having a bony skeleton typical of vertebrates. In order to understand why the various organisms display the features they do, it is necessary to consider what forces or historical constraints influence their genotypes and subsequent phenotypes.

It is logical to hypothesize that a streamlined shape is beneficial to swimming creatures, as is the structure of their appendages. This statement is itself an evolutionary hypothesis; it implies that streamlined individuals will be more successful than less streamlined ones and so will become prevalent in an aquatic environment. It may initially be difficult to reconcile the differences between the two aquatic forms swimming side-by-side with the similarities between one of them and the terrestrial species walking around on dry land. However, if it is understood that the whale is more closely related to the terrestrial deer than it is to the fish, much of the confusion disappears. Using this comparative approach, it is unnecessary, and scientifically unjustified, to construct an elaborate scenario whereby breathing air at the surface is more advantageous to a whale than gills would be; the simpler explanation is that the whale breathes air because it (like the deer) is a mammal, and both species inherited this trait from a common ancestor sometime in the past.

Organisms are thus a mixture of two kinds of traits. Ecological traits are those the particular form of which reflects long-term adaptation to the species’ habitat. Two species living in the same habitat might then be expected to be similar in such features and different from species in other habitats. Evolutionary characteristics, on the other hand, indicate common ancestry rather than common ecology. Here, similarity between two species indicates that they are related to each other through common ancestry, just as familial similarity can be used to identify siblings in a crowd of people. In reality, all traits are somewhere along a continuum between these two extremes, but this distinction highlights the importance of understanding the evolutionary history of organisms and traits. The value of an evolutionary perspective comes from its comparative and historical basis, which allows biologists to place their snapshot-in-time observations within the broader context of the continuous history of life.

Early Evolutionary Thought

Underlying evolutionary theory is Mendelian genetics, which provides a mechanism whereby genes conferring advantageous traits can be passed on to offspring. Both Mendelian genetics and the theory of evolution are, at first glance (and in retrospect), remarkably simple. The theory of evolution, however, is paradoxical in that it leads to extremely complex predictions and thus is often misunderstood, misinterpreted, and misapplied.

It is important to distinguish between the phenomenon of evolution and the various processes or mechanisms that may lead to evolution. The idea that species might be mutable, or subject to change over generations, dates back to at least the mid-eighteenth century, when the French naturalist Georges-Louis Leclerc, comte de Buffon, the Swiss naturalist Charles Bonnet, and even the Swedish botanist Carolus Linnaeus
suggested that species (or at least “varieties”) might be modified over time by intrinsic biological or extrinsic environmental factors. Other biologists after that time also promoted the idea that populations and species could evolve. Nevertheless, with the publication of
On the Origin of Species by Means of Natural Selection

in 1859, Charles Darwin
became the most prominent of those who proposed that all species had descended from a common ancestor and that there was a single “tree of life.” These claims regarding the history of evolution, however, are distinct from the problem of how, or through what mechanisms, evolution occurs.

In the first decade of the nineteenth century, Jean-Baptiste Lamarck
promoted a hypothesis of inheritance of acquired characteristics to explain how species could adapt over time to their environments. His famous giraffe example illustrates the Lamarckian view: Individual giraffes acquire longer necks as a result of reaching for leaves high on trees, then pass that modified characteristic to their offspring. According to Lamarck’s theories, as a result of such adaptation, the species—and, in fact, each individual member of the species—is modified over time. While completely in line with early nineteenth century views of inheritance, this view of the mechanism of evolution has since been shown to be incorrect.

Darwinian Evolution: Natural Selection

In the mid-nineteenth century, Darwin and Alfred Russel Wallace
independently developed the theory of evolution via natural selection, a theory that is consistent with the principles of inheritance as described by Gregor Mendel. Both Darwin’s and Wallace’s arguments center on four observations of nature and a logical conclusion derived from those observations (presented here in standard genetics terminology, although Darwin and Wallace used different terms).

First, variation exists in the phenotypes of different individuals in a population. Second, some portion of that variation is heritable, or capable of being passed from parents to offspring. Third, more individuals are produced in a population than will survive and reproduce. Fourth, some individuals are, because of their particular phenotypes, better able to survive and reproduce than others. From this, Darwin and Wallace deduced that because certain individuals have inherited variations that confer on them a greater ability to survive and reproduce than others, these better-adapted individuals are more likely to transmit their genetically inherited traits to the next generation. Therefore, the frequency of individuals with the favored inherited traits would increase in the next generation, though each individual’s genetic constitution would remain unchanged throughout its lifetime. This process would continue as long as new genetic variants continued to arise and selection favored some over others. The theory of natural selection provided a workable and independently testable natural mechanism by which evolution of complex and sometimes very different
adaptations could occur within and among species.

Evolutionary Biology after Darwin

Despite their theoretical insight, Darwin and Wallace had an incomplete and partially incorrect understanding of the genetic basis of inheritance. Mendel published his work describing the fundamental principles of inheritance in 1866 (he had reported the results before the Brünn Natural History Society earlier, in February and March of 1865), but Darwin and Wallace were unaware throughout their lives that the correct mechanism of inheritance had been discovered. In fact, Mendel’s work went almost entirely unnoticed by the scientific community for thirty-four years; it was rediscovered, and its significance appreciated, in the first decade of the twentieth century. Over the next three decades of the twentieth century, theoreticians integrated Darwin’s theory of natural selection with the principles of genetics discovered by Mendel and others. Simultaneously, Ernst Mayr,
G. Ledyard Stebbins,
George Gaylord Simpson, and Julian Huxley
demonstrated that the evolution of species and the patterns in the fossil record were consistent with each other and could be readily explained by Darwinian principles. This effort culminated in the 1930s and 1940s in the “modern synthesis,” a fusion of thought that resulted in the development of the field of population genetics, a discipline in which biologists seek to describe and predict, quantitatively, evolutionary changes in populations of sexually reproducing organisms.

Since the modern synthesis (also called the neo-Darwinian synthesis), biologists have concentrated their efforts on applying the theories of population genetics to understand the evolutionary dynamics of particular groups of organisms. More recently, techniques of phylogenetic systematics have been developed to provide a means of reconstructing phylogenetic relationships among species. This effort has emphasized the need for a comparative and evolutionary approach to general biology, which is essential to correct interpretation of biological classification.

In the 1960s, Motoo Kimura proposed the neutral theory of evolution, which challenged the “selectionist” view that patterns of genetic and phenotypic variation in most traits are determined by natural selection. The “neutralist” view maintains that much genetic variation, especially that seen in the numerous alleles of enzyme-coding genes, has little effect on fitness and therefore must be controlled by mechanisms other than selection. Advances in molecular biology, particularly those from genomics projects, have allowed testing of the selectionist and neutralist views and have provided evidence that natural selection has a powerful effect on certain variations in DNA, whereas other variations in DNA are subject to neutral evolution. An ongoing effort for a unified model of evolution is integration of evolutionary theory with the understanding of the processes of development (dubbed “evo-devo”), a field that also has benefited greatly from genome projects.

Evolutionary Mechanisms

Natural selection as described by Darwin and Wallace leads to the evolution of adaptations. However, many traits (perhaps the majority) are not adaptations; that is, differences in the particular form of those traits from one member of the species to the next do not lead to differences in fitness among those individuals. Such traits are mostly uninfluenced by natural selection, yet they can and do evolve. Thus, there must be mechanisms beyond natural selection that lead to changes in the genetic structure of biological systems over time.

Evolutionary mechanisms are usually envisioned as acting on individual organisms within a population. For example, natural selection may eliminate some individuals while others survive and produce a large number of offspring genetically similar to themselves. As a result, evolution occurs within those populations. A key tenet of Darwinian evolution (which distinguishes it from Lamarckian evolution) is that populations evolve, but the individual organisms that constitute that population do not, in the sense that their genetic constitution remains essentially constant even though their environments may change. Although evolution of populations is certainly the most familiar scenario, this is not the only level at which evolution occurs.

Richard Dawkins
energized the scientific discussion of evolution with his book The Selfish Gene, first published in 1976. Dawkins argued that natural selection could operate on any type of “replicator,” or unit of biological organization that displayed a faithful but imperfect mechanism of copying itself and that had differing rates of survival and reproduction among the variant copies. Under this definition, it is possible to view individual genes or strands of DNA as focal points for evolutionary mechanisms such as selection. Dawkins used this framework to consider how the existence of DNA selected to maximize its chances of replication (or “selfish DNA”)
would influence the evolution of social behavior, communication, and even multicellularity.

Recognizing that biological systems are arranged in a hierarchical fashion from genes to genomes (or cells) to individuals through populations, species, and communities, Elisabeth Vrba and Niles Eldredge in 1984 proposed that evolutionary changes could occur in any collection of entities (such as populations) as a result of mechanisms acting on the entities (individuals) that make up that collection. Because each level in the biological hierarchy (at least above that of genes) has as its building blocks the elements of the preceding one, evolution may occur within any of them. Vrba and Eldredge further argued that evolution could be viewed as resulting from two general kinds of mechanisms: those that introduce genetic variation and those that sort whatever variation is available. At each level, there are processes that introduce and sort variation, though they may have different names depending on the level being discussed.

Natural selection is a sorting process. Other mechanisms that sort genetic variation include sexual selection, whereby certain variants are favored based on their ability to enhance reproductive success (though not necessarily survival), and genetic drift, which is especially important in small populations. Although these forces are potentially strong engines for driving changes in genetic structure, their action—and therefore the direction and magnitude of evolutionary changes that they can cause—is constrained by the types of variation available and the extent to which that variation is genetically controlled.

Processes such as mutation, recombination, development, migration, and hybridization introduce variation at one or more levels in the biological hierarchy. Of these, mutation is ultimately the most important, as changes in DNA sequences constitute the raw material for evolution at all levels. Without mutation, there would be no variation and thus no evolution. Nevertheless, mutation alone is a relatively weak evolutionary force, only really significant in driving evolutionary changes when coupled with processes of selection or genetic drift that can quickly change allele frequencies. Recombination, development, migration, and hybridization introduce new patterns of genetic variation (initially derived from the mutation of individual genes) at the genome, multicellular-organism, population, and species levels, respectively.

The Reality of Evolution

It is impossible to absolutely prove that descent with modification from a common ancestor is responsible for the diversity of life on earth. In fact, this dilemma of absolute proof exists for all scientific theories; as a result, science proceeds by constructing and testing potential explanations, gradually accepting those best supported by the accumulation of observation and evidence, and their logical interpretations, until theories are either clearly refuted or replaced by modified theories more consistent with the data.

Darwin’s concept of a single tree of life is supported by vast amounts of scientific evidence. In fact, the theory of evolution is among the most thoroughly tested and best-supported theories in all of science. The view that evolution has and continues to occur is not debated by biologists; there is simply too much evidence to support its existence across every biological discipline.

On a small scale, it is possible to demonstrate evolutionary changes experimentally or through direct observation. Spontaneous mutations that introduce genetic variation are well documented; the origination and spread of drug-resistant forms of viruses, bacteria, and other pathogens is clear evidence of this potential. Agricultural breeding programs and other types of artificial selection demonstrate that the genetic structure of lineages containing heritable variation can be changed over time through agents of selection. For example, work by John Doebley begun in the late 1980s suggested that the evolution of corn from a wild ancestor resembling modern teosinte may have involved changes in as few as five major genes and that this transition likely occurred as a result of domestication processes established in Mexico between seven thousand and ten thousand years ago. The effects of natural selection can likewise be observed in operation: Peter Grant and his colleagues discovered that during drought periods, when seed is limited, deep-billed individuals of the Galápagos Island finch Geospiza fortis increase in proportion to the general population of the species, as only the deep-billed birds can crack the large seeds remaining after the supply of smaller seeds is exhausted. These and similar examples demonstrate that the evolutionary mechanisms put forward by Darwin and others do occur and lead to microevolution, or evolutionary change within single species.

Attempts to account for larger-scale macroevolutionary patterns, such as speciation
and the origin of major groups of organisms, rely to some extent on direct observation but for the most part are based on indirect tests using morphological and genetic comparisons among different species, observed geographic distributions of species, and the fossil record. Such comparative studies rely on the concept of homology, the presence of corresponding and similarly constructed features among species, as well as similar DNA sequences and chromosomal rearrangements, which are a consequence of inheritance from common ancestry.

At the most basic level, organization of the genetic code is remarkably similar across species; only minor variations exist among organisms as diverse as archaea (bacteria found in extreme environments such as hot springs, salt lakes, and habitats lacking in oxygen), bacteria, and eukaryotes (organisms whose cells contain a true nucleus, including plants, animals, fungi, and their unicellular counterparts). This genetic homology extends as well to the presence of shared and similarly functioning gene sequences across biological taxa, such as homeotic genes, common within major groups of eukaryotes. The near-universal nature of the genetic code can be best explained if it arose once during the early evolution of the first forms of life and has been transmitted through inheritance and preserved through natural selection to the present in all organisms.

Morphological homologies are also widespread; the limbs of mammals, birds, amphibians, and reptiles, for example, are all built out of the same fundamental arrangement of bones. The particular shapes, and even number, of these bones can vary among groups, often as adaptations to the widely varying functions of these bones. For example, if the bones in the pectoral fins of dolphins are compared to the bones in the human arm and hand, the same arrangement of bones is immediately evident but the bones differ in their relative sizes in accordance with the different functions of these forelimbs.

Genetic, cytological, and molecular studies have greatly enhanced the understanding of evolution. In general, these studies support previously reconstructed evolutionary histories derived from anatomical comparisons, geographic distributions, and the fossil record, while refining many of the details and clarifying the molecular mechanisms of evolution. As methods for chemical staining and microscopic examination of chromosomes were developed, cytologists noticed that the chromosomes of related species are highly similar and, in many cases, can be aligned with one another. The aligned chromosomes of related species, however, frequently differ by noticeable rearrangements, such as inversions, translocations, fusions, and fissions. For instance, human and chimpanzee chromosomes differ by nine inversions and one chromosome fusion. Molecular evidence has revealed that the fusion and two of the inversions happened in the human ancestral lineage, whereas seven of the inversions happened in the chimpanzee ancestral lineage since the two lineages diverged from common ancestry. Comparative chromosomal analyses have allowed
scientists to reconstruct the chromosomal constitutions of several now-extinct common ancestral species.

Genome projects have generated massive amounts of DNA sequence data that reveal in exquisite detail the molecular evolutionary history of genomes. As an example, at least eight primate genomes (human, chimpanzee, gorilla, and rhesus macaque, among others) have been sequenced and annotated. They show that gene duplication followed by mutational divergence is a principal mechanism for the evolution of new genes. Pseudogenes
(nonfunctional, mutated copies of genes) are as numerous as functional genes in these genomes, and millions of transposable elements constitute approximately 43 percent of their DNA. Nearly all genes, pseudogenes, and transposable elements are in the same chromosomal locations in all three of these genomes, indicating that they arose in a common ancestor. Those that differ are highly similar to functional genes or currently active transposable elements, evidence that they arose recently, since the divergences of these species’ lineages from common ancestry.

The conclusion that emerges from this weight of independent evidence is that structural, chromosomal, and genomic homologies reflect an underlying evolutionary homology, or descent from common ancestry.

Punctuated Equilibrium

Although the order of appearance of organisms in the fossil record is consistent with evolutionary theory in general, evolution does not always proceed in a gradual, predictable way. Paleontologists have long emphasized that gradualism—that is, evolution by gradual changes proceeding at more or less a constant rate, eventually producing major changes—is often not supported by the fossil record. The fossil record more often shows a pattern of relatively minor change over long periods of time, punctuated by much shorter periods of rapid change. Stephen Jay Gould
and Niles Eldredge, both paleontologists, offered a hypothesis called punctuated equilibrium to explain this discrepancy.

Gould and Eldredge’s hypothesis recognizes the fact that the fossil record shows long periods of relative stasis (little change) punctuated by periods of rapid change, and consider this the principal mode for evolution. Instead of the strict neo-Darwinian view of gradual changes leading to large changes over time, Gould and Eldredge suggest that large changes are the result of a series of larger steps over a much shorter period of time. When first proposed, the punctuated equilibrium theory was subject to considerable skepticism, but it has gained more acceptance over time.

The Practice of Evolutionary Biology

Contemporary evolutionary biology builds upon the theoretical foundations of Darwinian evolution by natural selection, the modern synthesis of Darwinian evolution with Mendelian inheritance, augmentation of evolutionary theory with research on its mechanisms and processes, such as punctuated equilibrium and biological development, and integration of an enormous body of data from molecular studies and genome projects. Although the reality of evolution is no longer in doubt, considerable research is underway on the relative importance of various evolutionary mechanisms in the history of particular groups of organisms. Much effort continues to be directed at reconstructing the particular historical path that life on earth has taken and that has led to the enormous diversity of species in the past and present. Likewise, scientists seek a fuller understanding of how new species arise, as the process of speciation represents a watershed event separating microevolution and macroevolution.

Unlike many other fields of biology, evolutionary biology is not always amenable to tests of simple cause-and-effect hypotheses. Much of what evolutionary biologists are interested in understanding occurred in the past and over vast periods of time. In addition, the evolutionary outcomes observed in nature depend on such a large number of environmental, biological, and random factors that re-creating and studying the circumstances that could have led to a particular outcome is virtually impossible. Finally, organisms are complex creatures exposed to conflicting evolutionary pressures, such as the need to attract mates while simultaneously attempting to remain hidden from predators; such compromise-type situations are hard to simulate under experimental conditions.

Many evolutionary studies rely on making predictions about the patterns one would expect to observe in nature if evolution in one form or another were to have occurred, and such studies often involve synthesis of data derived from fieldwork, theoretical modeling, and laboratory analysis. While such indirect tests of evolutionary hypotheses are not based on the sort of controlled data that are generated in direct experiments, if employed appropriately the indirect tests can be equally valid and powerful. Their strength comes from the ability to formulate predictions based on one species or type of data that may then be supported or refuted by examining additional species or data from another area of biology. In this way, evolutionary biologists are able to use the history of life on earth as a natural experiment, and, like forensic scientists, to piece together clues to solve the greatest biological mystery of all.

Key Terms




adaptation


:

a genetically based characteristic that confers on an organism the ability to survive and reproduce under prevailing environmental conditions




evolution

:

the process of change in the genetic structure of a population over time; descent with modification




fitness

:

the relative reproductive contribution of one individual to the next generation as compared to that of others in the population





genetic drift


:

chance fluctuations in allele frequencies within a population, resulting from random processes in gamete formation and sampling, and variation in the number and genotypes of offspring produced by different individuals




genotype

:

the genetic constitution of an individual or group





natural selection


:

the phenomenon of differing survival and reproduction rates among various genotypes in response to external factors; the frequencies of alleles carried by favored genotypes, and the phenotypes conferred by those alleles, increase in succeeding generations





phylogeny


:

the history of descent of a group of species from a common ancestor





Bibliography

Carroll, Sean B. Endless Forms Most Beautiful: The New Science of Evo Devo. New York: Norton, 2006. Print.

Carroll, Sean B. The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution. New York: Norton, 2007. Print.

Coyne, Jerry A. Why Evolution Is True. New York: Viking, 2009. Print.

Darwin, Charles. On the Origin of Species by Means of Natural Selection. 1859. Reprint. New York: Mod. Lib., 1998. Print.

Dawkins, Richard. The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe without Design. New York: Norton, 1996. Print.

Dawkins, Richard. Climbing Mount Improbable. New York: Norton, 1997. Print.

Dawkins, Richard. The Selfish Gene. 30th anniv. ed. New York: Oxford UP, 2009. Print.

Eldredge, Niles, and Stephen Jay Gould. “Punctuated Equilibria: An Alternative to Phyletic Gradualism.” Models in Paleobiology. Ed. Thomas J. M. Schopf. San Francisco: Freeman, 1972. Print.

Fairbanks, Daniel J. Relics of Eden: The Powerful Evidence of Evolution in Human DNA. Amherst: Prometheus, 2007. Print.

Freeman, Scott, and Jon C. Herron. Evolutionary Analysis. 5th ed. San Francisco: Cummings, 2012. Print.

Gould, Stephen Jay. Eight Little Piggies. New York: Norton, 1994. Print.

Pontarotti, Pierre. Evolutionary Biology: Exobiology and Evolutionary Mechanisms. New York: Springer, 2013. Print.

Quammen, David. Song of the Dodo. New York: Simon, 1997. Print.

Singh, Rama S., and Costas B. Krimbas, eds. Evolutionary Genetics: From Molecules to Morphology. New York: Cambridge UP, 2000. Print.

Soyer, Orkun S. Evolutionary Systems Biology. New York: Springer, 2012. Print.

Weiner, Jonathan. The Beak of the Finch: A Story of Evolution in Our Time. New York: Random, 1995. Print.