Microbial Phylogeny

Processes and Patterns of Evolution

Natural selection can only occur in the presence of genetic variation; environmental conditions determine which traits are selected.

Learning Objectives

Explain why only heritable variation can be acted upon by natural selection

Key Takeaways

Key Points

  • Genetic variation within a population is a result of mutations and sexual reproduction.
  • A mutation may be neutral, reduce an organism’s fitness, or increase an organism’s fitness.
  • An adaptation is a heritable trait that increases the survival and rate of reproduction of an organism in its present environment.
  • Divergent evolution describes the process in which two species evolve in diverse directions from a common point.
  • Convergent evolution is the process in which similar traits evolve independently in species that do not share a recent common ancestry.

Key Terms

  • adaptation: modification of something or its parts that makes it more fit for existence under the conditions of its current environment
  • divergent evolution: the process by which a species with similar traits become groups that are tremendously different from each other over many generations
  • convergent evolution: a trait of evolution in which species not of similar recent origin acquire similar properties due to natural selection


Natural selection can only take place if there is variation, or differences, among individuals in a population. Importantly, these differences must have some genetic basis; otherwise, the selection will not lead to change in the next generation. This is critical because variation among individuals can be caused by non-genetic reasons, such as an individual being taller due to better nutrition rather than different genes.

Genetic diversity within a population comes from two main mechanisms: mutation and sexual reproduction. Mutation, a change in the DNA sequence, is the ultimate source of new alleles, or new genetic variation in any population. The genetic changes caused by mutation can have one of three outcomes:

  • Many mutations will have no effect on the fitness of the phenotype; these are called neutral mutations.
  • A mutation may affect the phenotype of the organism in a way that gives it reduced fitness (a lower likelihood of survival or fewer offspring).
  • A mutation may produce a phenotype with a beneficial effect on fitness. Different mutations will have a range of effects on the fitness of an organism that expresses them in their phenotype, from a small effect to a great effect.

Sexual reproduction also leads to genetic diversity: when two parents reproduce, unique combinations of alleles assemble to produce the unique genotypes and thus phenotypes in each of the offspring. However, sexual reproduction can not lead to new genes, but rather provides a new combination of genes in a given individual.


A heritable trait that aids the survival and reproduction of an organism in its present environment is called an adaptation. Scientists describe groups of organisms becoming adapted to their environment when a change in the range of genetic variation occurs over time that increases or maintains the “fitness” of the population to its environment. The webbed feet of platypuses are an adaptation for swimming. The snow leopards’ thick fur is an adaptation for living in the cold. The cheetahs’ fast speed is an adaptation for catching prey.

Whether or not a trait is favorable depends on the environmental conditions at the time. The same traits are not always selected because environmental conditions can change. For example, consider a species of plant that grew in a moist climate and did not need to conserve water. Large leaves were selected because they allowed the plant to obtain more energy from the sun. Large leaves require more water to maintain than small leaves, and the moist environment provided favorable conditions to support large leaves. After thousands of years, the climate changed and the area no longer had excess water. The direction of natural selection shifted so that plants with small leaves were selected because those populations were able to conserve water to survive the new environmental conditions.

The evolution of species has resulted in enormous variation in form and function. Sometimes, evolution gives rise to groups of organisms that become tremendously different from each other. When two species evolve in diverse directions from a common point, it is called divergent evolution. Such divergent evolution can be seen in the forms of the reproductive organs of flowering plants which share the same basic anatomies; however, they can look very different as a result of selection in different physical environments and adaptation to different kinds of pollinators.


Flowering Plants: Flowering plants evolved from a common ancestor. Notice that the (a) dense blazing star (Liatrus spicata) and the (b) purple coneflower (Echinacea purpurea) vary in appearance, yet both share a similar basic morphology.

In other cases, similar phenotypes evolve independently in distantly-related species. For example, flight has evolved in both bats and insects; they both have structures we refer to as wings, which are adaptations to flight. However, the wings of bats and insects have evolved from very different original structures. This phenomenon is called convergent evolution, where similar traits evolve independently in species that do not share a recent common ancestry. The two species came to the same function, flying, but did so separately from each other.

These physical changes occur over enormous spans of time and help explain how evolution occurs. Natural selection acts on individual organisms, which in turn can shape an entire species. Although natural selection may work in a single generation on an individual, it can take thousands or even millions of years for the genotype of an entire species to evolve. It is over these large time spans that life on earth has changed and continues to change.

Distinguishing between Similar Traits

Similar traits can be either homologous structures that share an embryonic origin or analogous structures that share a function.

Learning Objectives

Explain the difference between homologous and analogous structures

Key Takeaways

Key Points

  • Organisms may be very closely related, even though they look quite different, due to a minor genetic change that caused a major morphological difference.
  • Unrelated organisms may appear very similar because both organisms developed common adaptations that evolved within similar environmental conditions.
  • To determine the phylogeny of an organism, scientists must determine whether a similarity is homologous or analogous.
  • The advancement of DNA technology, the area of molecular systematics, describes the use of information on the molecular level, including DNA analysis.

Key Terms

  • analogous: when similar similar physical features occur in organisms because of environmental constraints and not due to a close evolutionary relationship
  • homologous: when similar physical features and genomes stem from developmental similarities that are based on evolution
  • phylogeny: the evolutionary history of an organism
  • molecular systematics: molecular phylogenetics is the analysis of hereditary molecular differences, mainly in DNA sequences, to gain information on an organism’s evolutionary relationships

Two Options for Similarities

In general, organisms that share similar physical features and genomes tend to be more closely related than those that do not. Such features that overlap both morphologically (in form) and genetically are referred to as homologous structures; they stem from developmental similarities that are based on evolution. For example, the bones in the wings of bats and birds have homologous structures.


Homologous structures: Bat and bird wings are homologous structures, indicating that bats and birds share a common evolutionary past.

Notice it is not simply a single bone, but rather a grouping of several bones arranged in a similar way. The more complex the feature, the more probable that any overlap is due to a common evolutionary past. Imagine two people from different countries both inventing a car with all the same parts and in exactly the same arrangement without any previous or shared knowledge. That outcome would be highly improbable. However, if two people both invented a hammer, it would be reasonable to conclude that both could have the original idea without the help of the other. The same relationship between complexity and shared evolutionary history is true for homologous structures in organisms.

Misleading Appearances

Some organisms may be very closely related, even though a minor genetic change caused a major morphological difference to make them look quite different. Similarly, unrelated organisms may be distantly related, but appear very similar. This usually happens because both organisms developed common adaptations that evolved within similar environmental conditions. When similar characteristics occur because of environmental constraints and not due to a close evolutionary relationship, it is called an analogy or homoplasy. For example, insects use wings to fly like bats and birds, but the wing structure and embryonic origin is completely different. These are called analogous structures.


Analogous structures: The (c) wing of a honeybee is similar in shape to a (b) bird wing and (a) bat wing, and it serves the same function. However, the honeybee wing is not composed of bones and has a distinctly-different structure and embryonic origin. These wing types (insect versus bat and bird) illustrate an analogy: similar structures that do not share an evolutionary history.

Similar traits can be either homologous or analogous. Homologous structures share a similar embryonic origin; analogous organs have a similar function. For example, the bones in the front flipper of a whale are homologous to the bones in the human arm. These structures are not analogous. The wings of a butterfly and the wings of a bird are analogous, but not homologous. Some structures are both analogous and homologous: the wings of a bird and the wings of a bat are both homologous and analogous. Scientists must determine which type of similarity a feature exhibits to decipher the phylogeny of the organisms being studied.

Molecular Comparisons

With the advancement of DNA technology, the area of molecular systematics, which describes the use of information on the molecular level including DNA analysis, has blossomed. New computer programs not only confirm many earlier classified organisms, but also uncover previously-made errors. As with physical characteristics, even the DNA sequence can be tricky to read in some cases. For some situations, two very closely-related organisms can appear unrelated if a mutation occurred that caused a shift in the genetic code. An insertion or deletion mutation would move each nucleotide base over one place, causing two similar codes to appear unrelated.

Sometimes two segments of DNA code in distantly-related organisms randomly share a high percentage of bases in the same locations, causing these organisms to appear closely related when they are not. For both of these situations, computer technologies have been developed to help identify the actual relationships. Ultimately, the coupled use of both morphologic and molecular information is more effective in determining phylogeny.

The Levels of Classification

Taxanomic classification divides species in a hierarchical system beginning with a domain and ending with a single species.

Learning Objectives

Describe how taxonomic classification of organisms is accomplished and detail the levels of taxonomic classification from domain to species

Key Takeaways

Key Points

  • Categories within taxonomic classification are arranged in increasing specificity.
  • The most general category in taxonomic classification is domain, which is the point of origin for all species; all species belong to one of these domains: Bacteria, Archaea, and Eukarya.
  • Within each of the three domains, we find kingdoms, the second category within taxonomic classification, followed by subsequent categories that include phylum, class, order, family, genus, and species.
  • At each classification category, organisms become more similar because they are more closely related.
  • As scientific technology advances, changes to the taxonomic classification of many species must be altered as inaccuracies in classifications are discovered and corrected.

Key Terms

  • binomial nomenclature: the scientific system of naming each species of organism with a Latinized name in two parts
  • taxon: any of the taxonomic categories such as phylum or subspecies
  • Linnaeus: Swedish botanist, physician and zoologist who laid the foundations for the modern scheme of nomenclature; known as the “father of modern taxonomy”

The Levels of Classification

Taxonomy (which literally means “arrangement law”) is the science of classifying organisms to construct internationally-shared classification systems with each organism placed into more and more inclusive groupings. Think about how a grocery store is organized. One large space is divided into departments, such as produce, dairy, and meats. Then each department further divides into aisles, then each aisle into categories and brands, and then, finally, a single product. This organization from larger to smaller, more-specific categories is called a hierarchical system.


Hierarchical models: The taxonomic classification system uses a hierarchical model to organize living organisms into increasingly specific categories. The common dog, Canis lupus familiaris, is a subspecies of Canis lupus, which also includes the wolf and dingo.

The taxonomic classification system (also called the Linnaean system after its inventor, Carl Linnaeus, a Swedish botanist, zoologist, and physician) uses a hierarchical model. Moving from the point of origin, the groups become more specific, until one branch ends as a single species. For example, after the common beginning of all life, scientists divide organisms into three large categories called domains: Bacteria, Archaea, and Eukarya. Within each domain is a second category called a kingdom. After kingdoms, the subsequent categories of increasing specificity are: phylum, class, order, family, genus, and species.


Levels in taxonomic classification: At each sublevel in the taxonomic classification system, organisms become more similar. Dogs and wolves are the same species because they can breed and produce viable offspring, but they are different enough to be classified as different subspecies.

The kingdom Animalia stems from the Eukarya domain. The full name of an organism technically has eight terms. For dogs, it is: Eukarya, Animalia, Chordata, Mammalia, Carnivora, Canidae, Canis, and lupus. Notice that each name is capitalized except for species and that genus and species names are italicized. Scientists generally refer to an organism only by its genus and species, which is its two-word scientific name, in what is called binomial nomenclature. Therefore, the scientific name of the dog is Canis lupus. The name at each level is also called a taxon. In other words, dogs are in order Carnivora. Carnivora is the name of the taxon at the order level; Canidae is the taxon at the family level, and so forth. Organisms also have a common name that people typically use; in this case, dog. Note that the dog is additionally a subspecies: the “familiaris” in Canis lupus familiaris. Subspecies are members of the same species that are capable of mating and reproducing viable offspring, but they are considered separate subspecies due to geographic or behavioral isolation or other factors.

Dogs actually share a domain (Eukarya) with the widest diversity of organisms, including plants and butterflies. At each sublevel, the organisms become more similar because they are more closely related. Historically, scientists classified organisms using physical characteristics, but as DNA technology developed, more precise phylogenies have been determined.

Recent genetic analysis and other advancements have found that some earlier phylogenetic classifications do not align with the evolutionary past; therefore, changes and updates must be made as new discoveries occur. Recall that phylogenetic trees are hypotheses and are modified as data becomes available. In addition, classification historically has focused on grouping organisms mainly by shared characteristics and does not necessarily illustrate how the various groups relate to each other from an evolutionary perspective. For example, despite the fact that a hippopotamus resembles a pig more than a whale, the hippopotamus may be the closest living relative to the whale.