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15.8.3: Perspectives on the Phylogenetic Tree - Biology


15.8.3: Perspectives on the Phylogenetic Tree

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. Scientists did not consider the concept of genes transferring between unrelated species as a possibility until relatively recently. Horizontal gene transfer (HGT), or lateral gene transfer, is the transfer of genes between unrelated species. HGT is an ever-present phenomenon, with many evolutionists postulating a major role for this process in evolution, thus complicating the simple tree model. Genes pass between species which are only distantly related using standard phylogeny, thus adding a layer of complexity to understanding phylogenetic relationships.

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


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. Scientists did not consider the concept of genes transferring between unrelated species as a possibility until relatively recently. Horizontal gene transfer (HGT), or lateral gene transfer, is the transfer of genes between unrelated species. HGT is an ever-present phenomenon, with many evolutionists postulating a major role for this process in evolution, thus complicating the simple tree model. Genes pass between species which are only distantly related using standard phylogeny, thus adding a layer of complexity to understanding phylogenetic relationships.

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


Genome Fusion and Eukaryote Evolution

Within the past decade, James Lake of the UCLA/NASA Astrobiology Institute proposed that the genome fusion process is responsible for the evolution of the first eukaryotic cells (Figurea). Using DNA analysis and a new mathematical algorithm, 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. Alternatively, this work is new and the CR algorithm is relatively unsubstantiated, which causes many scientists to resist this hypothesis.

Lake's more recent work (Figureb) proposes that gram-negative bacteria, which are unique within their domain in that they contain two lipid bilayer membranes, 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. Scientists have also used this mechanism to explain the double membranes in mitochondria and chloroplasts. Lake’s work is not without skepticism, and the biological science community still debates his ideas. 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.

The scientific community now widely accepts the theory that mitochondria and chloroplasts are endosymbiotic in origin. More controversial is the proposal that (a) the eukaryotic nucleus resulted from fusing archaeal and bacterial genomes, and that (b) Gram-negative bacteria, which have two membranes, resulted from fusing Archaea and Gram-positive bacteria, each of which has a single membrane.

The nucleus-first hypothesis proposes that the nucleus evolved in prokaryotes first (Figurea), 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 (Figureb), 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 (Figurec). All of these hypotheses are testable. Only time and more experimentation will determine which hypothesis data best supports.

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.


20.3 Perspectives on the Phylogenetic Tree

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. he phylogenetic tree concept with a single trunk representing a shared ancestry, with the branches representing the divergence of species from this ancestry, 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.

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).

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

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 10 13 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 mutated and the enzyme looses activity, the aphids revert back to their more common green color (Figure 20.13).

Everyday Connection for AP® Courses

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

  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. Some are skeptical of Lake’s work, and the biological science community still debates his ideas. 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.

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.

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.

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.

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.

The transfer of genes by a mechanism not involving asexual reproduction is called:

Particles that transfer genetic material from one species to another, especially in marine prokaryotes:

What does the trunk of the classic phylogenetic tree represent?

Which phylogenetic model proposes that all three domains of life evolved from a pool of primitive prokaryotes?

Compare three different ways that eukaryotic cells may have evolved.

Some hypotheses propose that mitochondria were acquired first, followed by the development of the nucleus. Others propose that the nucleus evolved first and that this new eukaryotic cell later acquired the mitochondria. Still others hypothesize that prokaryotes descended from eukaryotes by the loss of genes and complexity.

Describe how aphids acquired the ability to change color.

Aphids have acquired the ability to make the carotenoids on their own. DNA analysis has demonstrated that this ability is due to the transfer of fungal genes into the insect by HGT, presumably as the insect consumed fungi for food.

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    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 5a, 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 5b) with its multiple trunks as a phylogenetic to represent a diminished evolutionary role for HGT.

    Figure 5. 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 1. (credit b: modification of work by “psyberartist”/Flickr)


    29 Perspectives on the Phylogenetic Tree

    By the end of this section, you will be able to do the following:

    • Describe horizontal gene transfer
    • Illustrate how prokaryotes and eukaryotes transfer genes horizontally
    • Identify the web and ring models of phylogenetic relationships and describe how they differ from the original phylogenetic tree concept

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

    Many phylogenetic trees are models of the evolutionary relationship among species. Phylogenetic trees originated with Charles Darwin, who sketched the first phylogenetic tree in 1837 ((Figure)a). This served as a prototype for subsequent studies for more than a century. The phylogenetic tree concept 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)b). However, evidence from modern DNA sequence analysis and newly developed computer algorithms has caused skepticism about the standard tree model’s validity in the scientific community.


    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. Scientists did not consider the concept of genes transferring between unrelated species as a possibility until relatively recently. Horizontal gene transfer (HGT), or lateral gene transfer, is the transfer of genes between unrelated species. HGT is an ever-present phenomenon, with many evolutionists postulating a major role for this process in evolution, thus complicating the simple tree model. Genes pass between species which are only distantly related using standard phylogeny, thus adding a layer of complexity to understanding phylogenetic relationships.

    The various ways that HGT occurs in prokaryotes is important to understanding phylogenies. Although at present some do not view HGT as important to eukaryotic evolution, HGT does occur in this domain as well. Finally, as an example of the ultimate gene transfer, some scientists have proposed genome fusion theories between symbiotic or endosymbiotic organisms 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. Scientists believe that HGT is more prevalent in prokaryotes, but that this process transfers only about 2% of the prokaryotic genome. Some researchers believe such estimates are premature: we must view the actual importance of HGT to evolutionary processes as a work in progress. As scientists investigate this phenomenon more thoroughly, they may reveal more HGT transfer. Many scientists believe that HGT and mutation are (especially in prokaryotes) a significant source of genetic variation, which is the raw material in the natural selection process. These transfers may occur between any two species that share an intimate relationship ((Figure)).

    Prokaryotic and Eukaryotic HGT Mechanisms Summary
    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

    HGT in Prokaryotes

    HGT mechanisms are quite common in the Bacteria and Archaea domains, thus significantly changing the way scientists view their evolution. 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 Endosymbiont Theory purports that the eukaryotes’ mitochondria and the green plants’ chloroplasts and flagellates originated as free-living prokaryotes that invaded primitive eukaryotic cells and become established as permanent symbionts in the cytoplasm.

    Microbiology students are well aware that genes transfer among common bacteria. These gene transfers between species are the major mechanism whereby bacteria acquire resistance to antibiotics. Classically, scientists believe that three different mechanisms drive such transfers.

    1. Transformation: bacteria takes up naked DNA
    2. Transduction: a virus transfers the genes
    3. Conjugation: a hollow tube, or pilus transfers genes between organisms

    More recently, scientists have discovered a fourth gene transfer mechanism between prokaryotes. Small, virus-like particles, or gene transfer agents (GTAs) transfer random genomic segments from one prokaryote species to another. GTAs are responsible for genetic changes, sometimes at a very high frequency compared to other evolutionary processes. Scientists characterized the first GTA in 1974 using purple, non-sulfur bacteria. These GTAs, which are most likely bacteriophages that lost the ability to reproduce on their own, carry random DNA pieces from one organism to another. Controlled studies using marine bacteria have demonstrated GTAs’ ability to act with high frequency. Scientists have estimated gene transfer events in marine prokaryotes, either by GTAs or by viruses, to be as high as 10 13 per year in the Mediterranean Sea alone. GTAs and viruses are 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 (located in many genes’ promoter region), the discovery that some eukaryotic genes were more homologous with bacterial DNA than Archaea DNA made this idea less tenable. Furthermore, scientists have proposed genome fusion from Archaea and Bacteria by endosymbiosis as the ultimate event in eukaryotic evolution.

    HGT in Eukaryotes

    Although it is easy to see how prokaryotes exchange genetic material by HGT, scientists initially thought that this process was absent in eukaryotes. After all, prokaryotes are but single cells exposed directly to their environment whereas, the multicellular organisms’ sex cells 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. Scientists believe this process is rarer in eukaryotes and has a much smaller evolutionary impact than in prokaryotes. In spite of this, HGT between distantly related organisms is evident in several eukaryotic species, and it is possible that scientists will discover more examples in the future.

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

    In animals, a particularly interesting example of HGT occurs within the aphid species ((Figure)). Aphids are insects that vary in color based on carotenoid content. Carotenoids are pigments that a variety of plants, fungi, and microbes produce, 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. Alternatively, aphids have acquired the ability to make the carotenoids on their own. According to DNA analysis, this ability is due to fungal genes transferring into the insect by HGT, presumably as the insect consumed fungi for food. A carotenoid enzyme, or desaturase, is responsible for the red coloration in certain aphids, and when mutation activates this gene, the aphids revert to their more common green color ((Figure)).


    Genome Fusion and Eukaryote Evolution

    Scientists believe the ultimate in HGT occurs through genome fusion between different prokaryote species when two symbiotic organisms become endosymbiotic. This occurs when one species is taken inside another species’ cytoplasm, 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 most biologists accept as the mechanism whereby eukaryotic cells obtained their mitochondria and chloroplasts. However, the role of endosymbiosis in developing the nucleus is more controversial. Scientists believe that nuclear and mitochondrial DNA have different (separate) evolutionary origins, with the mitochondrial DNA derived from the bacteria’s circular genomes ancient prokaryotic cells engulfed. We can regard mitochondrial DNA 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 sperm’s flagellum fails to enter the egg.

    Within the past decade, James Lake of the UCLA/NASA Astrobiology Institute proposed that the genome fusion process is responsible for the evolution of the first eukaryotic cells ((Figure)a). Using DNA analysis and a new mathematical algorithm, 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. Alternatively, this work is new and the CR algorithm is relatively unsubstantiated, which causes many scientists to resist this hypothesis.

    Lake’s more recent work ((Figure)b) proposes that gram-negative bacteria, which are unique within their domain in that they contain two lipid bilayer membranes, 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. Scientists have also used this mechanism to explain the double membranes in mitochondria and chloroplasts. Lake’s work is not without skepticism, and the biological science community still debates his ideas. 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.


    The nucleus-first hypothesis proposes that the nucleus evolved in prokaryotes first ((Figure)a), 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)b), 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)c). All of these hypotheses are testable. Only time and more experimentation will determine which hypothesis data best supports.


    Web and Network Models

    Recognizing the importance of HGT, especially in prokaryote evolution, 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 (Figure)a shows, 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. Scientists often call this model the “ web of life .” In an effort to save the tree analogy, some have proposed using the Ficus tree ((Figure)b) with its multiple trunks as a phylogenetic way to represent a diminished evolutionary role for HGT.


    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)). This is 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.


    In summary, we must modify Darwin’s “tree of life” model to include HGT. Does this mean abandoning the tree model completely? Even Lake argues that scientists should attempt to modify 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 phylogenetic tree concept is too simple, but made sense based on what scientists knew at the time. However, the search for a more useful model moves on: each model serves as hypotheses to test with the possibility of developing new models. This is how science advances. Researchers use these models as visualizations to help construct hypothetical evolutionary relationships and understand the massive amount of data that requires analysis.

    Section Summary

    The phylogenetic tree, which Darwin first used, is the classic “tree of life” model describing phylogenetic relationships among species, and the most common model that scientists use today. New ideas about HGT and genome fusion have caused some to suggest revising the model to resemble webs or rings.

    Review Questions

    The transfer of genes by a mechanism not involving asexual reproduction is called:

    Particles that transfer genetic material from one species to another, especially in marine prokaryotes:

    1. horizontal gene transfer
    2. lateral gene transfer
    3. genome fusion device
    4. gene transfer agents

    What does the trunk of the classic phylogenetic tree represent?

    1. single common ancestor
    2. pool of ancestral organisms
    3. new species
    4. old species

    Which phylogenetic model proposes that all three domains of life evolved from a pool of primitive prokaryotes?

    Critical Thinking Questions

    Compare three different ways that eukaryotic cells may have evolved.

    Some hypotheses propose that mitochondria were acquired first, followed by the development of the nucleus. Others propose that the nucleus evolved first and that this new eukaryotic cell later acquired the mitochondria. Still others hypothesize that prokaryotes descended from eukaryotes by the loss of genes and complexity.

    Describe how aphids acquired the ability to change color.

    Aphids have acquired the ability to make the carotenoids on their own. DNA analysis has demonstrated that this ability is due to the transfer of fungal genes into the insect by HGT, presumably as the insect consumed fungi for food.


    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 [link]a, 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 ([link]b) with its multiple trunks as a phylogenetic to represent a diminished evolutionary role for HGT.



    15.8.3: Perspectives on the Phylogenetic Tree - Biology

    By the end of this section, you will be able to do the following:

    • Describe horizontal gene transfer
    • Illustrate how prokaryotes and eukaryotes transfer genes horizontally
    • Identify the web and ring models of phylogenetic relationships and describe how they differ from the original phylogenetic tree concept

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

    Many phylogenetic trees are models of the evolutionary relationship among species. Phylogenetic trees originated with Charles Darwin, who sketched the first phylogenetic tree in 1837 ((Figure)a). This served as a prototype for subsequent studies for more than a century. The phylogenetic tree concept 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)b). However, evidence from modern DNA sequence analysis and newly developed computer algorithms has caused skepticism about the standard tree model’s validity in the scientific community.

    Figure 1. The (a) concept of the “tree of life” dates to an 1837 Charles Darwin sketch. 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. Scientists did not consider the concept of genes transferring between unrelated species as a possibility until relatively recently. Horizontal gene transfer (HGT), or lateral gene transfer, is the transfer of genes between unrelated species. HGT is an ever-present phenomenon, with many evolutionists postulating a major role for this process in evolution, thus complicating the simple tree model. Genes pass between species which are only distantly related using standard phylogeny, thus adding a layer of complexity to understanding phylogenetic relationships.

    The various ways that HGT occurs in prokaryotes is important to understanding phylogenies. Although at present some do not view HGT as important to eukaryotic evolution, HGT does occur in this domain as well. Finally, as an example of the ultimate gene transfer, some scientists have proposed genome fusion theories between symbiotic or endosymbiotic organisms 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. Scientists believe that HGT is more prevalent in prokaryotes, but that this process transfers only about 2% of the prokaryotic genome. Some researchers believe such estimates are premature: we must view the actual importance of HGT to evolutionary processes as a work in progress. As scientists investigate this phenomenon more thoroughly, they may reveal more HGT transfer. Many scientists believe that HGT and mutation are (especially in prokaryotes) a significant source of genetic variation, which is the raw material in the natural selection process. These transfers may occur between any two species that share an intimate relationship ((Figure)).

    Prokaryotic and Eukaryotic HGT Mechanisms Summary
    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

    HGT in Prokaryotes

    HGT mechanisms are quite common in the Bacteria and Archaea domains, thus significantly changing the way scientists view their evolution. 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 Endosymbiont Theory purports that the eukaryotes’ mitochondria and the green plants’ chloroplasts and flagellates originated as free-living prokaryotes that invaded primitive eukaryotic cells and become established as permanent symbionts in the cytoplasm.

    Microbiology students are well aware that genes transfer among common bacteria. These gene transfers between species are the major mechanism whereby bacteria acquire resistance to antibiotics. Classically, scientists believe that three different mechanisms drive such transfers.

    1. Transformation: bacteria takes up naked DNA
    2. Transduction: a virus transfers the genes
    3. Conjugation: a hollow tube, or pilus transfers genes between organisms

    More recently, scientists have discovered a fourth gene transfer mechanism between prokaryotes. Small, virus-like particles, or gene transfer agents (GTAs) transfer random genomic segments from one prokaryote species to another. GTAs are responsible for genetic changes, sometimes at a very high frequency compared to other evolutionary processes. Scientists characterized the first GTA in 1974 using purple, non-sulfur bacteria. These GTAs, which are most likely bacteriophages that lost the ability to reproduce on their own, carry random DNA pieces from one organism to another. Controlled studies using marine bacteria have demonstrated GTAs’ ability to act with high frequency. Scientists have estimated gene transfer events in marine prokaryotes, either by GTAs or by viruses, to be as high as 10 13 per year in the Mediterranean Sea alone. GTAs and viruses are 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 (located in many genes’ promoter region), the discovery that some eukaryotic genes were more homologous with bacterial DNA than Archaea DNA made this idea less tenable. Furthermore, scientists have proposed genome fusion from Archaea and Bacteria by endosymbiosis as the ultimate event in eukaryotic evolution.

    HGT in Eukaryotes

    Although it is easy to see how prokaryotes exchange genetic material by HGT, scientists initially thought that this process was absent in eukaryotes. After all, prokaryotes are but single cells exposed directly to their environment whereas, the multicellular organisms’ sex cells 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. Scientists believe this process is rarer in eukaryotes and has a much smaller evolutionary impact than in prokaryotes. In spite of this, HGT between distantly related organisms is evident in several eukaryotic species, and it is possible that scientists will discover more examples in the future.

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

    In animals, a particularly interesting example of HGT occurs within the aphid species ((Figure)). Aphids are insects that vary in color based on carotenoid content. Carotenoids are pigments that a variety of plants, fungi, and microbes produce, 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. Alternatively, aphids have acquired the ability to make the carotenoids on their own. According to DNA analysis, this ability is due to fungal genes transferring into the insect by HGT, presumably as the insect consumed fungi for food. A carotenoid enzyme, or desaturase, is responsible for the red coloration in certain aphids, and when mutation activates this gene, the aphids revert to their more common green color ((Figure)).

    Figure 2. (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 mutation inactivates the genes for making carotenoids, the aphids revert back to (b) their green color. Red coloration makes the aphids considerably 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)

    Genome Fusion and Eukaryote Evolution

    Scientists believe the ultimate in HGT occurs through genome fusion between different prokaryote species when two symbiotic organisms become endosymbiotic. This occurs when one species is taken inside another species’ cytoplasm, 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 most biologists accept as the mechanism whereby eukaryotic cells obtained their mitochondria and chloroplasts. However, the role of endosymbiosis in developing the nucleus is more controversial. Scientists believe that nuclear and mitochondrial DNA have different (separate) evolutionary origins, with the mitochondrial DNA derived from the bacteria’s circular genomes ancient prokaryotic cells engulfed. We can regard mitochondrial DNA 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 sperm’s flagellum fails to enter the egg.

    Within the past decade, James Lake of the UCLA/NASA Astrobiology Institute proposed that the genome fusion process is responsible for the evolution of the first eukaryotic cells ((Figure)a). Using DNA analysis and a new mathematical algorithm, 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. Alternatively, this work is new and the CR algorithm is relatively unsubstantiated, which causes many scientists to resist this hypothesis.

    Lake’s more recent work ((Figure)b) proposes that gram-negative bacteria, which are unique within their domain in that they contain two lipid bilayer membranes, 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. Scientists have also used this mechanism to explain the double membranes in mitochondria and chloroplasts. Lake’s work is not without skepticism, and the biological science community still debates his ideas. 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.

    Figure 3. The scientific community now widely accepts the theory that mitochondria and chloroplasts are endosymbiotic in origin. More controversial is the proposal that (a) the eukaryotic nucleus resulted from fusing archaeal and bacterial genomes, and that (b) Gram-negative bacteria, which have two membranes, resulted from fusing 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)a), 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)b), 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)c). All of these hypotheses are testable. Only time and more experimentation will determine which hypothesis data best supports.

    Figure 4. 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

    Recognizing the importance of HGT, especially in prokaryote evolution, 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 (Figure)a shows, 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. Scientists often call this model the “web of life.” In an effort to save the tree analogy, some have proposed using the Ficus tree ((Figure)b) with its multiple trunks as a phylogenetic way to represent a diminished evolutionary role for HGT.

    Figure 5. In W. Ford Doolittle’s (a) phylogenetic model, 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 an oak’s single trunk similar to Darwin’s tree in (Figure). (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)). This is 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.

    Figure 6. According to the “ring of life” phylogenetic model, the three domains of life evolved from a pool of primitive prokaryotes.

    In summary, we must modify Darwin’s “tree of life” model to include HGT. Does this mean abandoning the tree model completely? Even Lake argues that scientists should attempt to modify 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 phylogenetic tree concept is too simple, but made sense based on what scientists knew at the time. However, the search for a more useful model moves on: each model serves as hypotheses to test with the possibility of developing new models. This is how science advances. Researchers use these models as visualizations to help construct hypothetical evolutionary relationships and understand the massive amount of data that requires analysis.

    Section Summary

    The phylogenetic tree, which Darwin first used, is the classic “tree of life” model describing phylogenetic relationships among species, and the most common model that scientists use today. New ideas about HGT and genome fusion have caused some to suggest revising the model to resemble webs or rings.

    Review Questions

    The transfer of genes by a mechanism not involving asexual reproduction is called:


    Results

    The ggtreeExtra package implemented a layer function, geom_fruit, which is a universal function that aligns graphic layers to a phylogenetic tree ( fig. 1A supplementary table S1 , Supplementary Material online). It can internally reorder associated data based on the structure of a phylogenetic tree, visualize the data using specific geometric layer function with user-provided aesthetic mapping and nonvariable setting, and the graphic layer will be displayed with the tree side by side (i.e., right-hand side for rectangular layout or external ring for circular layout fig. 1C) with perfect alignment. Different data graph layers can be added to a tree progressively. For example, geom_fruit is able to display a heatmap and a bar plot to the outer rings of an annotated phylogenetic tree to compare microbial abundance across different body sites of humans ( supplementary fig. S7 , Supplementary Material online). These two layers were automatically aligned to the circular phylogenetic tree and were displayed on different external rings. The number of external rings is not strictly limited and the user is free to visualize several associated data sets using different geometric layers on different external rings. Each data set is visualized on an independent ring layer, and multiple ring layers are stacked on a circular phylogenetic tree, which makes the ggtreeExtra package particularly useful for layering different data sets to create highly informative tree graphics. For example, multiple heatmaps and bar chart layers were compactly displayed on the circular tree to represent the status of the gene, metabolic capacity, and genome size of 963 bacteria and archaea species ( supplementary fig. S8 , Supplementary Material online).

    The design and features of the ggtreeExtra package. (A) The overall design of the ggtreeExtra package (B) comparison of visualization methods for tree annotation (i.e., tree and data graphic alignment) supported by ggtreeExtra and other tools (C) visualizing associated data (e.g., distribution of species abundance as boxplot) with a phylogenetic tree side by side or on the external ring (inset on the left) (D) using subplots and images as insets on a phylogenetic tree to present taxon-specific structural feature and summary statistics (E) illustration of representing multidimensional data sets on an inward circular phylogenetic tree with chord diagram incorporated to display inter-relationships. The ggtreeExtra package supports both rectangular and circular layouts and allows transformation between different layouts (C). Multiple data sets can be integrated and a variable can be mapped to visual characteristics to visualize another type of data (CDE), such as using taxon information to color silhouette images (D).

    The design and features of the ggtreeExtra package. (A) The overall design of the ggtreeExtra package (B) comparison of visualization methods for tree annotation (i.e., tree and data graphic alignment) supported by ggtreeExtra and other tools (C) visualizing associated data (e.g., distribution of species abundance as boxplot) with a phylogenetic tree side by side or on the external ring (inset on the left) (D) using subplots and images as insets on a phylogenetic tree to present taxon-specific structural feature and summary statistics (E) illustration of representing multidimensional data sets on an inward circular phylogenetic tree with chord diagram incorporated to display inter-relationships. The ggtreeExtra package supports both rectangular and circular layouts and allows transformation between different layouts (C). Multiple data sets can be integrated and a variable can be mapped to visual characteristics to visualize another type of data (CDE), such as using taxon information to color silhouette images (D).

    Unlike other tools, ggtreeExtra was developed based on the grammar of graphics ( Wilkinson 2012) and allowed users to map variables of associated data to visual attributes of the outer ring graphic layer at a high level of abstraction ( supplementary figs. S3, S4, and S7 , Supplementary Material online). The geometric layers defined in ggplot2 ( Wickham 2016) and its extensions can be used in the geom_fruit function. For example, the geom_phylopic, implemented by the ggimage package, can be used to overlay silhouette images on the external layers to compare morphological characteristics with other attributes (e.g., taxonomy order, dietary preferences, and environmental variables) ( fig. 1D). With this feature, ggtreeExtra supports more data types and visualization methods than other tools, since the ggplot2 community has developed many geometric layers ( fig. 1B supplementary tables S1 and S2 , Supplementary Material online). For instance, taxon-specific infographics can be added as insets in ggtreeExtra using the geom_plot layer provided by the ggpmics package ( supplementary fig. S5A , Supplementary Material online). The ggtreeExtra package makes no assumption about user data. Given a suitable geometric layer, ggtreeExtra can incorporate and visualize any kind of information with a tree. This unique feature ensures the versatility of ggtreeExtra, making it easy to represent heterogeneous data from different disciplines.

    A unique advantage of the circular layout is to create a chord diagram to reveal complex relationships. Couple with the inward circular tree layout supported by ggtree ( Yu et al. 2017), ggtreeExtra allows displaying flows or connections between taxa, such as syntenic linkage among genes and genomes, and reticulate evolutionary relationships including horizontal gene transfer, hybridization, and interspecific recombination. This makes ggtreeExtra an ideal tool for exploring relationships or interactions between taxa in a compact way, and it is extremely powerful and uniquely suitable for microbiome research to present microbial correlation or interaction network with phylogenetic tree and other associated data. To demonstrate this unique feature, we used ggtreeExtra and ggtree ( Yu et al. 2017) to integrate and visualize several data sets from Arabidopsis leaf microbiome ( Bai et al. 2015) on the phylogenetic tree, including directional interactions among different bacteria strains, number of target genes, strain abundance, taxonomy information, and the biosynthetic potential of the isolates. The phylogenetic tree was visualized using an inward circular layout and the interaction data were visualized as a chord diagram connecting the corresponding isolates of the tree leaves. Other information was displayed as a stacked bar chart, heatmaps, and symbolic points on the tree ( fig. 1E). With ggtreeExtra incorporating all the information, some of the evolutionary patterns that are not straightforward might become more obvious. For example, in figure 1E, we can easily find that the inhibitor interactions are more widely observed at strains from Firmicutes and Gammaproteobacteria, whereas strains from Alphaproteobacteria and Betaproteobacteria prefer sensitivity interactions. After the subsequent Mann−Whitney U test, the number of different interactions among these strains was confirmed to be significant ( supplementary fig. S10 , Supplementary Material online). To our knowledge, there are no other software tools that can easily produce such the figure, and the visualization indeed help us explore the data and generate new insights as our findings were not revealed in the original paper ( Helfrich et al. 2018).

    The ggtreeExtra is a subpackage of the ggtree package suite and takes all the advantages of other ggtree subpackages. Phylogenetic data imported by the treeio ( Wang et al. 2020) package can be used in ggtreeExtra. This allows evolutionary inferences (e.g., clade support, molecular dating, and selection pressure) from commonly used software to be linked to other associated data (e.g., observational and experimental data) for integrative and comparative study ( supplementary fig. S6 , Supplementary Material online). Tree data can be processed using the tidytree package and a phylogenetic tree visualized by ggtree with fully annotation can be further annotated in ggtreeExtra with data layers especially in circular layout ( supplementary figs. S5−S8 , Supplementary Material online fig. 1E). The ggtreeExtra package extends the capabilities of ggtree and fully supports the grammar of graphics implemented in ggplot2 ( Wickham 2016) ( fig. 1A). It supports aesthetic mapping ( supplementary figs. S3−S6 , Supplementary Material online) and a layered grammar of graphics ( supplementary figs. S7−S9 , Supplementary Material online). Users can use scale functions to specify how the data were mapped to visual values and theme functions to adjust graphic appearance ( supplementary figs. S3−S9 , Supplementary Material online). Moreover, it takes all benefits of the ggplot2 community. Geometric layers defined in ggplot2 and other extension packages can be used in ggtreeExtra to visualize tree data ( supplementary table S2 and figs. S2−S5, Supplementary Material online). We proposed and implemented this framework design originally in ggtree ( Yu et al. 2018) and ggtreeExtra fully embraces the design concept. This is the beauty of the ggtree and ggtreeExtra and lays the foundation for displaying tree annotated data layers. It allows ggtreeExtra to support more visualization methods and has no assumption of the input data types (supplementary table S1 and S2, Supplementary Material online). As the ggplot2 community keeps expanding, there will be more methods implemented which can be employed to create tree data layers in ggtreeExtra. Furthermore, the combination of these methods allows ggtreeExtra to create more possibilities than other tools to integrate more diverse data sets for novel exploratory data analysis ( fig. 1B and E). Therefore, it has more potential to reveal systematic patterns and insights of our data than other tools. The versatility of this package ensures its applications in different research areas such as population genetics, molecular epidemiology and microbiome.


    Watch the video: Understanding Phylogenetic Trees (November 2021).