Skip to Content
OpenStax Logo
Biology for AP® Courses

20.3 Perspectives on the Phylogenetic Tree

Biology for AP® Courses20.3 Perspectives on the Phylogenetic Tree
Buy book
  1. Preface
  2. Unit 1
    1. 1 The Study of Life
      1. Introduction
      2. 1.1 The Science of Biology
      3. 1.2 Themes and Concepts of Biology
      4. Key Terms
      5. Chapter Summary
      6. Review Questions
      7. Critical Thinking Questions
      8. Test Prep for AP® Courses
    2. 2 The Chemical Foundation of Life
      1. Introduction
      2. 2.1 Atoms, Isotopes, Ions, and Molecules: The Building Blocks
      3. 2.2 Water
      4. 2.3 Carbon
      5. Key Terms
      6. Chapter Summary
      7. Review Questions
      8. Critical Thinking Questions
      9. Test Prep for AP® Courses
      10. Science Practice Challenge Questions
    3. 3 Biological Macromolecules
      1. Introduction
      2. 3.1 Synthesis of Biological Macromolecules
      3. 3.2 Carbohydrates
      4. 3.3 Lipids
      5. 3.4 Proteins
      6. 3.5 Nucleic Acids
      7. Key Terms
      8. Chapter Summary
      9. Review Questions
      10. Critical Thinking Questions
      11. Test Prep for AP® Courses
      12. Science Practice Challenge Questions
  3. Unit 2
    1. 4 Cell Structure
      1. Introduction
      2. 4.1 Studying Cells
      3. 4.2 Prokaryotic Cells
      4. 4.3 Eukaryotic Cells
      5. 4.4 The Endomembrane System and Proteins
      6. 4.5 Cytoskeleton
      7. 4.6 Connections between Cells and Cellular Activities
      8. Key Terms
      9. Chapter Summary
      10. Review Questions
      11. Critical Thinking Questions
      12. Test Prep for AP® Courses
      13. Science Practice Challenge Questions
    2. 5 Structure and Function of Plasma Membranes
      1. Introduction
      2. 5.1 Components and Structure
      3. 5.2 Passive Transport
      4. 5.3 Active Transport
      5. 5.4 Bulk Transport
      6. Key Terms
      7. Chapter Summary
      8. Review Questions
      9. Critical Thinking Questions
      10. Test Prep for AP® Courses
      11. Science Practice Challenge Questions
    3. 6 Metabolism
      1. Introduction
      2. 6.1 Energy and Metabolism
      3. 6.2 Potential, Kinetic, Free, and Activation Energy
      4. 6.3 The Laws of Thermodynamics
      5. 6.4 ATP: Adenosine Triphosphate
      6. 6.5 Enzymes
      7. Key Terms
      8. Chapter Summary
      9. Review Questions
      10. Critical Thinking Questions
      11. Test Prep for AP® Courses
      12. Science Practice Challenge Questions
    4. 7 Cellular Respiration
      1. Introduction
      2. 7.1 Energy in Living Systems
      3. 7.2 Glycolysis
      4. 7.3 Oxidation of Pyruvate and the Citric Acid Cycle
      5. 7.4 Oxidative Phosphorylation
      6. 7.5 Metabolism without Oxygen
      7. 7.6 Connections of Carbohydrate, Protein, and Lipid Metabolic Pathways
      8. 7.7 Regulation of Cellular Respiration
      9. Key Terms
      10. Chapter Summary
      11. Review Questions
      12. Critical Thinking Questions
      13. Test Prep for AP® Courses
      14. Science Practice Challenge Questions
    5. 8 Photosynthesis
      1. Introduction
      2. 8.1 Overview of Photosynthesis
      3. 8.2 The Light-Dependent Reaction of Photosynthesis
      4. 8.3 Using Light to Make Organic Molecules
      5. Key Terms
      6. Chapter Summary
      7. Review Questions
      8. Critical Thinking Questions
      9. Test Prep for AP® Courses
      10. Science Practice Challenge Questions
    6. 9 Cell Communication
      1. Introduction
      2. 9.1 Signaling Molecules and Cellular Receptors
      3. 9.2 Propagation of the Signal
      4. 9.3 Response to the Signal
      5. 9.4 Signaling in Single-Celled Organisms
      6. Key Terms
      7. Chapter Summary
      8. Review Questions
      9. Critical Thinking Questions
      10. Test Prep for AP® Courses
      11. Science Practice Challenge Questions
    7. 10 Cell Reproduction
      1. Introduction
      2. 10.1 Cell Division
      3. 10.2 The Cell Cycle
      4. 10.3 Control of the Cell Cycle
      5. 10.4 Cancer and the Cell Cycle
      6. 10.5 Prokaryotic Cell Division
      7. Key Terms
      8. Chapter Summary
      9. Review Questions
      10. Critical Thinking Questions
      11. Test Prep for AP® Courses
      12. Science Practice Challenge Questions
  4. Unit 3
    1. 11 Meiosis and Sexual Reproduction
      1. Introduction
      2. 11.1 The Process of Meiosis
      3. 11.2 Sexual Reproduction
      4. Key Terms
      5. Chapter Summary
      6. Review Questions
      7. Critical Thinking Questions
      8. Test Prep for AP® Courses
      9. Science Practice Challenge Questions
    2. 12 Mendel's Experiments and Heredity
      1. Introduction
      2. 12.1 Mendel’s Experiments and the Laws of Probability
      3. 12.2 Characteristics and Traits
      4. 12.3 Laws of Inheritance
      5. Key Terms
      6. Chapter Summary
      7. Review Questions
      8. Critical Thinking Questions
      9. Test Prep for AP® Courses
      10. Science Practice Challenge Questions
    3. 13 Modern Understandings of Inheritance
      1. Introduction
      2. 13.1 Chromosomal Theory and Genetic Linkages
      3. 13.2 Chromosomal Basis of Inherited Disorders
      4. Key Terms
      5. Chapter Summary
      6. Review Questions
      7. Critical Thinking Questions
      8. Test Prep for AP® Courses
      9. Science Practice Challenge Questions
    4. 14 DNA Structure and Function
      1. Introduction
      2. 14.1 Historical Basis of Modern Understanding
      3. 14.2 DNA Structure and Sequencing
      4. 14.3 Basics of DNA Replication
      5. 14.4 DNA Replication in Prokaryotes
      6. 14.5 DNA Replication in Eukaryotes
      7. 14.6 DNA Repair
      8. Key Terms
      9. Chapter Summary
      10. Review Questions
      11. Critical Thinking Questions
      12. Test Prep for AP® Courses
      13. Science Practice Challenge Questions
    5. 15 Genes and Proteins
      1. Introduction
      2. 15.1 The Genetic Code
      3. 15.2 Prokaryotic Transcription
      4. 15.3 Eukaryotic Transcription
      5. 15.4 RNA Processing in Eukaryotes
      6. 15.5 Ribosomes and Protein Synthesis
      7. Key Terms
      8. Chapter Summary
      9. Review Questions
      10. Critical Thinking Questions
      11. Test Prep for AP® Courses
      12. Science Practice Challenge Questions
    6. 16 Gene Regulation
      1. Introduction
      2. 16.1 Regulation of Gene Expression
      3. 16.2 Prokaryotic Gene Regulation
      4. 16.3 Eukaryotic Epigenetic Gene Regulation
      5. 16.4 Eukaryotic Transcriptional Gene Regulation
      6. 16.5 Eukaryotic Post-transcriptional Gene Regulation
      7. 16.6 Eukaryotic Translational and Post-translational Gene Regulation
      8. 16.7 Cancer and Gene Regulation
      9. Key Terms
      10. Chapter Summary
      11. Review Questions
      12. Critical Thinking Questions
      13. Test Prep for AP® Courses
      14. Science Practice Challenge Questions
    7. 17 Biotechnology and Genomics
      1. Introduction
      2. 17.1 Biotechnology
      3. 17.2 Mapping Genomes
      4. 17.3 Whole-Genome Sequencing
      5. 17.4 Applying Genomics
      6. 17.5 Genomics and Proteomics
      7. Key Terms
      8. Chapter Summary
      9. Review Questions
      10. Critical Thinking Questions
      11. Test Prep for AP® Courses
      12. Science Practice Challenge Questions
  5. Unit 4
    1. 18 Evolution and Origin of Species
      1. Introduction
      2. 18.1 Understanding Evolution
      3. 18.2 Formation of New Species
      4. 18.3 Reconnection and Rates of Speciation
      5. Key Terms
      6. Chapter Summary
      7. Review Questions
      8. Critical Thinking Questions
      9. Test Prep for AP® Courses
      10. Science Practice Challenge Questions
    2. 19 The Evolution of Populations
      1. Introduction
      2. 19.1 Population Evolution
      3. 19.2 Population Genetics
      4. 19.3 Adaptive Evolution
      5. Key Terms
      6. Chapter Summary
      7. Review Questions
      8. Critical Thinking Questions
      9. Test Prep for AP® Courses
      10. Science Practice Challenge Questions
    3. 20 Phylogenies and the History of Life
      1. Introduction
      2. 20.1 Organizing Life on Earth
      3. 20.2 Determining Evolutionary Relationships
      4. 20.3 Perspectives on the Phylogenetic Tree
      5. Key Terms
      6. Chapter Summary
      7. Review Questions
      8. Critical Thinking Questions
      9. Test Prep for AP® Courses
      10. Science Practice Challenge Questions
  6. Unit 5
    1. 21 Viruses
      1. Introduction
      2. 21.1 Viral Evolution, Morphology, and Classification
      3. 21.2 Virus Infection and Hosts
      4. 21.3 Prevention and Treatment of Viral Infections
      5. 21.4 Other Acellular Entities: Prions and Viroids
      6. Key Terms
      7. Chapter Summary
      8. Review Questions
      9. Critical Thinking Questions
      10. Test Prep for AP® Courses
      11. Science Practice Challenge Questions
    2. 22 Prokaryotes: Bacteria and Archaea
      1. Introduction
      2. 22.1 Prokaryotic Diversity
      3. 22.2 Structure of Prokaryotes
      4. 22.3 Prokaryotic Metabolism
      5. 22.4 Bacterial Diseases in Humans
      6. 22.5 Beneficial Prokaryotes
      7. Key Terms
      8. Chapter Summary
      9. Review Questions
      10. Critical Thinking Questions
      11. Test Prep for AP® Courses
      12. Science Practice Challenge Questions
  7. Unit 6
    1. 23 Plant Form and Physiology
      1. Introduction
      2. 23.1 The Plant Body
      3. 23.2 Stems
      4. 23.3 Roots
      5. 23.4 Leaves
      6. 23.5 Transport of Water and Solutes in Plants
      7. 23.6 Plant Sensory Systems and Responses
      8. Key Terms
      9. Chapter Summary
      10. Review Questions
      11. Critical Thinking Questions
      12. Test Prep for AP® Courses
      13. Science Practice Challenge Questions
  8. Unit 7
    1. 24 The Animal Body: Basic Form and Function
      1. Introduction
      2. 24.1 Animal Form and Function
      3. 24.2 Animal Primary Tissues
      4. 24.3 Homeostasis
      5. Key Terms
      6. Chapter Summary
      7. Review Questions
      8. Critical Thinking Questions
      9. Test Prep for AP® Courses
    2. 25 Animal Nutrition and the Digestive System
      1. Introduction
      2. 25.1 Digestive Systems
      3. 25.2 Nutrition and Energy Production
      4. 25.3 Digestive System Processes
      5. 25.4 Digestive System Regulation
      6. Key Terms
      7. Chapter Summary
      8. Review Questions
      9. Critical Thinking Questions
      10. Test Prep for AP® Courses
      11. Science Practice Challenge Questions
    3. 26 The Nervous System
      1. Introduction
      2. 26.1 Neurons and Glial Cells
      3. 26.2 How Neurons Communicate
      4. 26.3 The Central Nervous System
      5. 26.4 The Peripheral Nervous System
      6. 26.5 Nervous System Disorders
      7. Key Terms
      8. Chapter Summary
      9. Review Questions
      10. Critical Thinking Questions
      11. Test Prep for AP® Courses
      12. Science Practice Challenge Questions
    4. 27 Sensory Systems
      1. Introduction
      2. 27.1 Sensory Processes
      3. 27.2 Somatosensation
      4. 27.3 Taste and Smell
      5. 27.4 Hearing and Vestibular Sensation
      6. 27.5 Vision
      7. Key Terms
      8. Chapter Summary
      9. Review Questions
      10. Critical Thinking Questions
      11. Science Practice Challenge Questions
    5. 28 The Endocrine System
      1. Introduction
      2. 28.1 Types of Hormones
      3. 28.2 How Hormones Work
      4. 28.3 Regulation of Body Processes
      5. 28.4 Regulation of Hormone Production
      6. 28.5 Endocrine Glands
      7. Key Terms
      8. Chapter Summary
      9. Review Questions
      10. Critical Thinking Questions
      11. Test Prep for AP® Courses
      12. Science Practice Challenge Questions
    6. 29 The Musculoskeletal System
      1. Introduction
      2. 29.1 Types of Skeletal Systems
      3. 29.2 Bone
      4. 29.3 Joints and Skeletal Movement
      5. 29.4 Muscle Contraction and Locomotion
      6. Key Terms
      7. Chapter Summary
      8. Review Questions
      9. Critical Thinking Questions
      10. Science Practice Challenge Questions
    7. 30 The Respiratory System
      1. Introduction
      2. 30.1 Systems of Gas Exchange
      3. 30.2 Gas Exchange across Respiratory Surfaces
      4. 30.3 Breathing
      5. 30.4 Transport of Gases in Human Bodily Fluids
      6. Key Terms
      7. Chapter Summary
      8. Review Questions
      9. Critical Thinking Questions
      10. Test Prep for AP® Courses
      11. Science Practice Challenge Questions
    8. 31 The Circulatory System
      1. Introduction
      2. 31.1 Overview of the Circulatory System
      3. 31.2 Components of the Blood
      4. 31.3 Mammalian Heart and Blood Vessels
      5. 31.4 Blood Flow and Blood Pressure Regulation
      6. Key Terms
      7. Chapter Summary
      8. Review Questions
      9. Critical Thinking Questions
      10. Test Prep for AP® Courses
      11. Science Practice Challenge Questions
    9. 32 Osmotic Regulation and Excretion
      1. Introduction
      2. 32.1 Osmoregulation and Osmotic Balance
      3. 32.2 The Kidneys and Osmoregulatory Organs
      4. 32.3 Excretion Systems
      5. 32.4 Nitrogenous Wastes
      6. 32.5 Hormonal Control of Osmoregulatory Functions
      7. Key Terms
      8. Chapter Summary
      9. Review Questions
      10. Critical Thinking Questions
      11. Test Prep for AP® Courses
    10. 33 The Immune System
      1. Introduction
      2. 33.1 Innate Immune Response
      3. 33.2 Adaptive Immune Response
      4. 33.3 Antibodies
      5. 33.4 Disruptions in the Immune System
      6. Key Terms
      7. Chapter Summary
      8. Review Questions
      9. Critical Thinking Questions
      10. Test Prep for AP® Courses
      11. Science Practice Challenge Questions
    11. 34 Animal Reproduction and Development
      1. Introduction
      2. 34.1 Reproduction Methods
      3. 34.2 Fertilization
      4. 34.3 Human Reproductive Anatomy and Gametogenesis
      5. 34.4 Hormonal Control of Human Reproduction
      6. 34.5 Fertilization and Early Embryonic Development
      7. 34.6 Organogenesis and Vertebrate Formation
      8. 34.7 Human Pregnancy and Birth
      9. Key Terms
      10. Chapter Summary
      11. Review Questions
      12. Critical Thinking Questions
      13. Test Prep for AP® Courses
      14. Science Practice Challenge Questions
  9. Unit 8
    1. 35 Ecology and the Biosphere
      1. Introduction
      2. 35.1 The Scope of Ecology
      3. 35.2 Biogeography
      4. 35.3 Terrestrial Biomes
      5. 35.4 Aquatic Biomes
      6. 35.5 Climate and the Effects of Global Climate Change
      7. Key Terms
      8. Chapter Summary
      9. Review Questions
      10. Critical Thinking Questions
      11. Test Prep for AP® Courses
      12. Science Practice Challenge Questions
    2. 36 Population and Community Ecology
      1. Introduction
      2. 36.1 Population Demography
      3. 36.2 Life Histories and Natural Selection
      4. 36.3 Environmental Limits to Population Growth
      5. 36.4 Population Dynamics and Regulation
      6. 36.5 Human Population Growth
      7. 36.6 Community Ecology
      8. 36.7 Behavioral Biology: Proximate and Ultimate Causes of Behavior
      9. Key Terms
      10. Chapter Summary
      11. Review Questions
      12. Critical Thinking Questions
      13. Test Prep for AP® Courses
      14. Science Practice Challenge Questions
    3. 37 Ecosystems
      1. Introduction
      2. 37.1 Ecology for Ecosystems
      3. 37.2 Energy Flow through Ecosystems
      4. 37.3 Biogeochemical Cycles
      5. Key Terms
      6. Chapter Summary
      7. Review Questions
      8. Critical Thinking Questions
      9. Test Prep for AP® Courses
      10. Science Practice Challenge Questions
    4. 38 Conservation Biology and Biodiversity
      1. Introduction
      2. 38.1 The Biodiversity Crisis
      3. 38.2 The Importance of Biodiversity to Human Life
      4. 38.3 Threats to Biodiversity
      5. 38.4 Preserving Biodiversity
      6. Key Terms
      7. Chapter Summary
      8. Review Questions
      9. Critical Thinking Questions
      10. Test Prep for AP® Courses
  10. A | The Periodic Table of Elements
  11. B | Geological Time
  12. C | Measurements and the Metric System
  13. Index

In this section, you will explore the following questions:

  • What is horizontal gene transfer and its significance in constructing phylogenetic trees?
  • How do prokaryotes and eukaryotes transfer genes horizontally?
  • What are other models of phylogenetic relationships and how do they differ from the original phylogenetic tree concept?

Connection for AP® Courses

Newer technologies have uncovered surprising discoveries with unexpected relationships among organisms, such as the fact that humans seems to be more closely related to fungi than fungi are to plants. (Think about that the next time you see a mushroom). As the information about DNA sequences grows, scientists will become closer to mapping a more accurate evolutionary history of all life on Earth.

What makes phylogeny difficult, especially among prokaryotes, is the transfer of genes horizontally (horizontal gene transfer, or HGT) between unrelated species. Like mutations, HGT introduces genetic variation into the bacterial population. This passing of genes between species adds a layer of complexity to understanding relatedness.

Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP® Biology Curriculum Framework. The AP® Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP® Biology course, an inquiry-based laboratory experience, instructional activities, and AP® exam questions. A learning objective merges required content with one or more of the seven science practices.

Big Idea 1 The process of evolution drives the diversity and unity of life.
Enduring Understanding 1.B Organisms are linked by lines of descent from common ancestry.
Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today.
Science Practice 3.1 The student can pose scientific questions.
Learning Objective 1.14 The student is able to pose scientific questions that correctly identify essential properties of shared, core life processes that provide insight into the history of life on Earth.
Essential Knowledge 1.B.1 Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today.
Science Practice 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas.
Learning Objective 1.15 The student is able to describe specific examples of conserved core biological processes and features shared by all domains or within one domain of life, and how these shared, conserved core processes and features support the concept of common ancestry for all organisms.
Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes.
Enduring Understanding 3.C The processing of genetic information is imperfect and is a source of genetic variation.
Essential Knowledge 3.C.2 Biological systems have multiple processes that increase genetic variation.
Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices.
Learning Objective 3.27 The student is able to construct an explanation of processes that increase variation within a population.

The concepts of phylogenetic modeling are constantly changing. It is one of the most dynamic fields of study in all of biology. Over the last several decades, new research has challenged scientists’ ideas about how organisms are related. New models of these relationships have been proposed for consideration by the scientific community.

Many phylogenetic trees have been shown as models of the evolutionary relationship among species. Phylogenetic trees originated with Charles Darwin, who sketched the first phylogenetic tree in 1837 (Figure 20.12a), which served as a pattern for subsequent studies for more than a century. The concept of a phylogenetic tree with a single trunk representing a common ancestor, with the branches representing the divergence of species from this ancestor, fits well with the structure of many common trees, such as the oak (Figure 20.12b). However, evidence from modern DNA sequence analysis and newly developed computer algorithms has caused skepticism about the validity of the standard tree model in the scientific community.

 Image a shows Charles Darwin’s sketch of lines branching, like those on a tree. Photo b shows a photo of an oak tree with many branches.
Figure 20.12 The (a) concept of the “tree of life” goes back to an 1837 sketch by Charles Darwin. Like an (b) oak tree, the “tree of life” has a single trunk and many branches. (credit b: modification of work by "Amada44"/Wikimedia Commons)

Limitations to the Classic Model

Classical thinking about prokaryotic evolution, included in the classic tree model, is that species evolve clonally. That is, they produce offspring themselves with only random mutations causing the descent into the variety of modern-day and extinct species known to science. This view is somewhat complicated in eukaryotes that reproduce sexually, but the laws of Mendelian genetics explain the variation in offspring, again, to be a result of a mutation within the species. The concept of genes being transferred between unrelated species was not considered as a possibility until relatively recently. Horizontal gene transfer (HGT), also known as lateral gene transfer, is the transfer of genes between unrelated species. HGT has been shown to be an ever-present phenomenon, with many evolutionists postulating a major role for this process in evolution, thus complicating the simple tree model. Genes have been shown to be passed between species which are only distantly related using standard phylogeny, thus adding a layer of complexity to the understanding of phylogenetic relationships.

The various ways that HGT occurs in prokaryotes is important to understanding phylogenies. Although at present HGT is not viewed as important to eukaryotic evolution, HGT does occur in this domain as well. Finally, as an example of the ultimate gene transfer, theories of genome fusion between symbiotic or endosymbiotic organisms have been proposed to explain an event of great importance—the evolution of the first eukaryotic cell, without which humans could not have come into existence.

Horizontal Gene Transfer

Horizontal gene transfer (HGT) is the introduction of genetic material from one species to another species by mechanisms other than the vertical transmission from parent(s) to offspring. These transfers allow even distantly related species to share genes, influencing their phenotypes. It is thought that HGT is more prevalent in prokaryotes, but that only about 2% of the prokaryotic genome may be transferred by this process. Some researchers believe such estimates are premature: the actual importance of HGT to evolutionary processes must be viewed as a work in progress. As the phenomenon is investigated more thoroughly, it may be revealed to be more common. Many scientists believe that HGT and mutation appear to be (especially in prokaryotes) a significant source of genetic variation, which is the raw material for the process of natural selection. These transfers may occur between any two species that share an intimate relationship (Table 20.1).

Summary of Mechanisms of Prokaryotic and Eukaryotic HGT
Mechanism Mode of Transmission Example
Prokaryotes transformation DNA uptake many prokaryotes
transduction bacteriophage (virus) bacteria
conjugation pilus many prokaryotes
gene transfer agents phage-like particles purple non-sulfur bacteria
Eukaryotes from food organisms unknown aphid
jumping genes transposons rice and millet plants
epiphytes/parasites unknown yew tree fungi
from viral infections
Table 20.1

HGT in Prokaryotes

The mechanism of HGT has been shown to be quite common in the prokaryotic domains of Bacteria and Archaea, significantly changing the way their evolution is viewed. The majority of evolutionary models, such as in the Endosymbiont Theory, propose that eukaryotes descended from multiple prokaryotes, which makes HGT all the more important to understanding the phylogenetic relationships of all extant and extinct species.

The fact that genes are transferred among common bacteria is well known to microbiology students. These gene transfers between species are the major mechanism whereby bacteria acquire resistance to antibiotics. Classically, this type of transfer has been thought to occur by three different mechanisms:

  1. Transformation: naked DNA is taken up by a bacteria
  2. Transduction: genes are transferred using a virus
  3. Conjugation: the use a hollow tube called a pilus to transfer genes between organisms

More recently, a fourth mechanism of gene transfer between prokaryotes has been discovered. Small, virus-like particles called gene transfer agents (GTAs) transfer random genomic segments from one species of prokaryote to another. GTAs have been shown to be responsible for genetic changes, sometimes at a very high frequency compared to other evolutionary processes. The first GTA was characterized in 1974 using purple, non-sulfur bacteria. These GTAs, which are thought to be bacteriophages that lost the ability to reproduce on their own, carry random pieces of DNA from one organism to another. The ability of GTAs to act with high frequency has been demonstrated in controlled studies using marine bacteria. Gene transfer events in marine prokaryotes, either by GTAs or by viruses, have been estimated to be as high as 1013 per year in the Mediterranean Sea alone. GTAs and viruses are thought to be efficient HGT vehicles with a major impact on prokaryotic evolution.

As a consequence of this modern DNA analysis, the idea that eukaryotes evolved directly from Archaea has fallen out of favor. While eukaryotes share many features that are absent in bacteria, such as the TATA box (found in the promoter region of many genes), the discovery that some eukaryotic genes were more homologous with bacterial DNA than Archaea DNA made this idea less tenable. Furthermore, the fusion of genomes from Archaea and Bacteria by endosymbiosis has been proposed as the ultimate event in eukaryotic evolution.

HGT in Eukaryotes

Although it is easy to see how prokaryotes exchange genetic material by HGT, it was initially thought that this process was absent in eukaryotes. After all, prokaryotes are but single cells exposed directly to their environment, whereas the sex cells of multicellular organisms are usually sequestered in protected parts of the body. It follows from this idea that the gene transfers between multicellular eukaryotes should be more difficult. Indeed, it is thought that this process is rarer in eukaryotes and has a much smaller evolutionary impact than in prokaryotes. In spite of this fact, HGT between distantly related organisms has been demonstrated in several eukaryotic species, and it is possible that more examples will be discovered in the future.

In plants, gene transfer has been observed in species that cannot cross-pollinate by normal means. Transposons or “jumping genes” have been shown to transfer between rice and millet plant species. Furthermore, fungal species feeding on yew trees, from which the anti-cancer drug paclitaxel is derived from the bark, have acquired the ability to make paclitaxel themselves, a clear example of gene transfer.

In animals, a particularly interesting example of HGT occurs within the aphid species (Figure 20.13). Aphids are insects that vary in color based on carotenoid content. Carotenoids are pigments made by a variety of plants, fungi, and microbes, and they serve a variety of functions in animals, who obtain these chemicals from their food. Humans require carotenoids to synthesize vitamin A, and we obtain them by eating orange fruits and vegetables: carrots, apricots, mangoes, and sweet potatoes. On the other hand, aphids have acquired the ability to make the carotenoids on their own. According to DNA analysis, this ability is due to the transfer of fungal genes into the insect by HGT, presumably as the insect consumed fungi for food. A carotenoid enzyme called a desaturase is responsible for the red coloration seen in certain aphids, and it has been further shown that when this gene is inactivated by mutation, the aphids revert back to their more common green color (Figure 20.13).

Photo a shows small, oval-shaped red aphids crawling on a leaf. Photo b shows green aphids.
Figure 20.13 (a) Red aphids get their color from red carotenoid pigment. Genes necessary to make this pigment are present in certain fungi, and scientists speculate that aphids acquired these genes through HGT after consuming fungi for food. If genes for making carotenoids are inactivated by mutation, the aphids revert back to (b) their green color. Red coloration makes the aphids a lot more conspicuous to predators, but evidence suggests that red aphids are more resistant to insecticides than green ones. Thus, red aphids may be more fit to survive in some environments than green ones. (credit a: modification of work by Benny Mazur; credit b: modification of work by Mick Talbot)

Everyday Connection for AP® Courses

Barbara McClintock (1902–1992) discovered transposons while working on maize genetics.

A photo shows Barbara McClintock giving her Nobel Lecture.
Figure 20.14
What does the Eukaryote-first hypothesis suggest?
  1. that mitochondria were first established in a prokaryotic host which acquired a nucleus to become the first eukaryotic cell
  2. that the nucleus evolved in prokaryotes first followed by fusion of the new eukaryote with bacteria that became mitochondria
  3. that prokaryotes actually evolved from eukaryotes by losing genes and complexity
  4. that eukaryotes developed Golgi before mitochondria

Genome Fusion and the Evolution of Eukaryotes

Scientists believe the ultimate in HGT occurs through genome fusion between different species of prokaryotes when two symbiotic organisms become endosymbiotic. This occurs when one species is taken inside the cytoplasm of another species, which ultimately results in a genome consisting of genes from both the endosymbiont and the host. This mechanism is an aspect of the Endosymbiont Theory, which is accepted by a majority of biologists as the mechanism whereby eukaryotic cells obtained their mitochondria and chloroplasts. However, the role of endosymbiosis in the development of the nucleus is more controversial. Nuclear and mitochondrial DNA are thought to be of different (separate) evolutionary origin, with the mitochondrial DNA being derived from the circular genomes of bacteria that were engulfed by ancient prokaryotic cells. Mitochondrial DNA can be regarded as the smallest chromosome. Interestingly enough, mitochondrial DNA is inherited only from the mother. The mitochondrial DNA degrades in sperm when the sperm degrades in the fertilized egg or in other instances when the mitochondria located in the flagellum of the sperm fails to enter the egg.

Within the past decade, the process of genome fusion by endosymbiosis has been proposed by James Lake of the UCLA/NASA Astrobiology Institute to be responsible for the evolution of the first eukaryotic cells (Figure 20.15a). Using DNA analysis and a new mathematical algorithm called conditioned reconstruction (CR), his laboratory proposed that eukaryotic cells developed from an endosymbiotic gene fusion between two species, one an Archaea and the other a Bacteria. As mentioned, some eukaryotic genes resemble those of Archaea, whereas others resemble those from Bacteria. An endosymbiotic fusion event, such as Lake has proposed, would clearly explain this observation. On the other hand, this work is new and the CR algorithm is relatively unsubstantiated, which causes many scientists to resist this hypothesis.

More recent work by Lake (Figure 20.15b) proposes that gram-negative bacteria, which are unique within their domain in that they contain two lipid bilayer membranes, indeed resulted from an endosymbiotic fusion of archaeal and bacterial species. The double membrane would be a direct result of the endosymbiosis, with the endosymbiont picking up the second membrane from the host as it was internalized. This mechanism has also been used to explain the double membranes found in mitochondria and chloroplasts. Lake’s work is not without skepticism, and the ideas are still debated within the biological science community. In addition to Lake’s hypothesis, there are several other competing theories as to the origin of eukaryotes. How did the eukaryotic nucleus evolve? One theory is that the prokaryotic cells produced an additional membrane that surrounded the bacterial chromosome. Some bacteria have the DNA enclosed by two membranes; however, there is no evidence of a nucleolus or nuclear pores. Other proteobacteria also have membrane-bound chromosomes. If the eukaryotic nucleus evolved this way, we would expect one of the two types of prokaryotes to be more closely related to eukaryotes.

Part A shows a eukaryotic cell. The illustration indicates that, within the nucleus, operational genes were inherited from an ancestral Eubacteria, and informational genes were inherited from an ancestral Archaebacteria. Part B indicates that the outer membrane of Gram-negative bacteria is derived from Archaea, and the inner membrane is derived from Gram-positive bacteria.
Figure 20.15 The theory that mitochondria and chloroplasts are endosymbiotic in origin is now widely accepted. More controversial is the proposal that (a) the eukaryotic nucleus resulted from the fusion of archaeal and bacterial genomes, and that (b) Gram-negative bacteria, which have two membranes, resulted from the fusion of Archaea and Gram-positive bacteria, each of which has a single membrane.

The nucleus-first hypothesis proposes that the nucleus evolved in prokaryotes first (Figure 20.16a), followed by a later fusion of the new eukaryote with bacteria that became mitochondria. The mitochondria-first hypothesis proposes that mitochondria were first established in a prokaryotic host (Figure 20.16b), which subsequently acquired a nucleus, by fusion or other mechanisms, to become the first eukaryotic cell. Most interestingly, the eukaryote-first hypothesis proposes that prokaryotes actually evolved from eukaryotes by losing genes and complexity (Figure 20.16c). All of these hypotheses are testable. Only time and more experimentation will determine which hypothesis is best supported by data.

 Part A shows the nucleus-first hypothesis. According to this hypothesis, a primary endosymbiotic event resulted in an ancestral eukaryotic cell acquiring a nucleus, and a secondary endosymbiotic event resulted in the acquisition of a mitochondrion. Part B shows the mitochondrion-first hypothesis. According to this hypothesis, the mitochondrion was acquired before the nucleus, but both were acquired by endosymbiosis. Part C shows the eukaryote-first hypothesis. According to this hypothesis, prokaryotes evolved from eukaryotic cells that lost their nuclei and organelles.
Figure 20.16 Three alternate hypotheses of eukaryotic and prokaryotic evolution are (a) the nucleus-first hypothesis, (b) the mitochondrion-first hypothesis, and (c) the eukaryote-first hypothesis.

Web and Network Models

The recognition of the importance of HGT, especially in the evolution of prokaryotes, has caused some to propose abandoning the classic “tree of life” model. In 1999, W. Ford Doolittle proposed a phylogenetic model that resembles a web or a network more than a tree. The hypothesis is that eukaryotes evolved not from a single prokaryotic ancestor, but from a pool of many species that were sharing genes by HGT mechanisms. As shown in Figure 20.17a, some individual prokaryotes were responsible for transferring the bacteria that caused mitochondrial development to the new eukaryotes, whereas other species transferred the bacteria that gave rise to chloroplasts. This model is often called the “web of life.” In an effort to save the tree analogy, some have proposed using the Ficus tree (Figure 20.17b) with its multiple trunks as a phylogenetic to represent a diminished evolutionary role for HGT.

 Illustration (a) shows the web of life. The base of this web is an ancestral community of primitive cells. This pool of ancestral cells gave rise to the three domains of life. However, because of gene transfer and endosymbiosis events, connections occur between the branches at various points. Thus, eukaryotic chloroplasts and mitochondria originated in bacterial lineages, and archaea and bacteria have exchanged genes.
Figure 20.17 In the (a) phylogenetic model proposed by W. Ford Doolittle, the “tree of life” arose from a community of ancestral cells, has multiple trunks, and has connections between branches where horizontal gene transfer has occurred. Visually, this concept is better represented by (b) the multi-trunked Ficus than by the single trunk of the oak similar to the tree drawn by Darwin Figure 20.12. (credit b: modification of work by "psyberartist"/Flickr)

Ring of Life Models

Others have proposed abandoning any tree-like model of phylogeny in favor of a ring structure, the so-called “ring of life” (Figure 20.18); a phylogenetic model where all three domains of life evolved from a pool of primitive prokaryotes. Lake, again using the conditioned reconstruction algorithm, proposes a ring-like model in which species of all three domains—Archaea, Bacteria, and Eukarya—evolved from a single pool of gene-swapping prokaryotes. His laboratory proposes that this structure is the best fit for data from extensive DNA analyses performed in his laboratory, and that the ring model is the only one that adequately takes HGT and genomic fusion into account. However, other phylogeneticists remain highly skeptical of this model.

Illustration shows a ring with the words “pool of primitive prokaryotes” in the middle. Three arrows point outward from the ring, pointing at the three domains, Bacteria, Archaea, and Eukarya, indicating that all three domains arose from a common pool of prokaryotes.
Figure 20.18 According to the “ring of life” phylogenetic model, the three domains of life evolved from a pool of primitive prokaryotes.

In summary, the “tree of life” model proposed by Darwin must be modified to include HGT. Does this mean abandoning the tree model completely? Even Lake argues that all attempts should be made to discover some modification of the tree model to allow it to accurately fit his data, and only the inability to do so will sway people toward his ring proposal.

This doesn’t mean a tree, web, or a ring will correlate completely to an accurate description of phylogenetic relationships of life. A consequence of the new thinking about phylogenetic models is the idea that Darwin’s original conception of the phylogenetic tree is too simple, but made sense based on what was known at the time. However, the search for a more useful model moves on: each model serving as hypotheses to be tested with the possibility of developing new models. This is how science advances. These models are used as visualizations to help construct hypothetical evolutionary relationships and understand the massive amount of data being analyzed.

Citation/Attribution

Want to cite, share, or modify this book? This book is Creative Commons Attribution License 4.0 and you must attribute OpenStax.

Attribution information
  • If you are redistributing all or part of this book in a print format, then you must include on every physical page the following attribution:
    Access for free at https://openstax.org/books/biology-ap-courses/pages/1-introduction
  • If you are redistributing all or part of this book in a digital format, then you must include on every digital page view the following attribution:
    Access for free at https://openstax.org/books/biology-ap-courses/pages/1-introduction
Citation information

© Mar 8, 2018 OpenStax. Textbook content produced by OpenStax is licensed under a Creative Commons Attribution License 4.0 license. The OpenStax name, OpenStax logo, OpenStax book covers, OpenStax CNX name, and OpenStax CNX logo are not subject to the Creative Commons license and may not be reproduced without the prior and express written consent of Rice University.