Perspectives on the Phylogenetic Tree

Limitations to the Classic Model of Phylogenetic Trees

The concepts of phylogenetic modeling are constantly changing causing limitations to the classic model to arise.

Learning Objectives

Identify the limitations to the classic model of phylogenetic trees

Key Takeaways

Key Points

  • Charles Darwin sketched the first phylogenetic tree in 1837.
  • A single trunk on a phylogenetic tree represents a common ancestor and the branches represent the divergence of species from this ancestor.
  • Prokaryotes are assumed to evolve clonally in the classic tree model.
  • Horizontal gene transfer is the transfer of genes between unrelated species and, as such, complicates the simple tree model.
  • Ultimate gene transfer has provided theories of genome fusion between symbiotic or endosymbiotic organisms.

Key Terms

  • phylogenetic: of, or relating to the evolutionary development of organisms
  • clonal: pertaining to asexual reproduction
  • horizontal gene transfer: the transfer of genetic material from one organism to another one that is not its offspring; especially common among bacteria

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, 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. 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.

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Tree of life: 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.

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 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. 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 passing of genetic material between species by mechanisms other than from parent to offspring.

Learning Objectives

Explain how horizontal gene transfer can make resolution of phylogenies difficult

Key Takeaways

Key Points

  • It is thought that HGT is more prevalent in prokaryotes than eukaryotes, but that only about 2% of the prokaryotic genome may be transferred by this process.
  • 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.
  • HGT in prokaryotes occurs by four different mechanisms: transformation, transduction, conjugation, and via gene transfer agents.
  • HGT occurs in plants through transposons (jumping genes), which transfer between different species of plants.
  • An example of HGT in animals is the transfer (through consumption) of fungal genes into insects called aphids, which allows the aphids the ability to make carotenoids on their own.

Key Terms

  • transformation: the alteration of a bacterial cell caused by the transfer of DNA from another, especially if pathogenic
  • transduction: horizontal gene transfer mechanism in prokaryotes where genes are transferred using a virus
  • conjugation: the temporary fusion of organisms, especially as part of sexual reproduction

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 (using standard phylogeny) 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 these 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 evolutionists postulate a major role for this process in evolution, thus complicating the simple tree model. A number of 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, thus adding a layer of complexity to the understanding or resolution of phylogenetic relationships.

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Mechanisms of prokaryotic and eukaryotic horizontal gene transfer: Horizontal gene transfer 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 (using standard phylogeny) to share genes, influencing their phenotypes. Examples of mechanisms of horizontal gene transfer are listed for both prokaryotic and eukaryotic organisms.

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. These gene transfers between species are the major mechanism whereby bacteria acquire resistance to antibiotics. Classically, this type of transfer was thought to occur by three different mechanisms:

  • Transformation: naked DNA is taken up by a bacteria.
  • Transduction: genes are transferred using a virus.
  • 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.

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 only 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. 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 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. Aphids are insects that vary in color based on carotenoid content. Carotenoids are pigments made by a variety of plants, fungi, and microbes, which 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. Furthermore, it has been shown that when this gene is inactivated by mutation, the aphids revert back to their more common green color.

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HGT within the aphid species: (a) Red aphids get their color from red carotenoid pigment. Genes necessary to make this pigment are present in certain fungi. 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 much 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.

Endosymbiotic Theory and the Evolution of Eukaryotes

Genome fusion occurs during endosymbiosis, which is the mechanism proposed as responsible for the first eukaryotic cells.

Learning Objectives

Describe the genome fusion hypothesis and its relationship to the evolution of eukaryotes

Key Takeaways

Key Points

  • Two symbiotic organisms become endosymbiotic when one species is taken inside the cytoplasm of another species, resulting in genome fusion.
  • Genome fusion, by endosymbiosis, between two species, one an Archaea and the other a Bacteria, has been proposed as responsible for the evolution of the first eukaryotic cells.
  • Gram-negative bacteria are proposed to result from an endosymbiotic fusion of archaeal and bacterial species through a mechanism that has also been used to explain the double membranes found in mitochondria and chloroplasts.
  • The nucleus-first hypothesis proposes the nucleus evolved in prokaryotes first, followed by a later fusion of the new eukaryote with bacteria that became mitochondria.
  • The mitochondria-first hypothesis proposes mitochondria were first established in a prokaryotic host, which subsequently acquired a nucleus to become the first eukaryotic cell.
  • The eukaryote-first hypothesis proposes prokaryotes actually evolved from eukaryotes by losing genes and complexity.

Key Terms

  • genome fusion: a result of endosymbiosis when a genome consists of genes from both the endosymbiont and the host.
  • symbiotic: of a relationship with mutual benefit between two individuals or organisms
  • endosymbiosis: when one symbiotic species is taken inside the cytoplasm of another symbiotic species and both become endosymbiotic

Genome Fusion and the Evolution of Eukaryotes

Scientists believe the ultimate event in HGT (horizontal gene transfer) occurs through genome fusion between different species 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 to be responsible for the evolution of the first eukaryotic cells. Using DNA analysis and a new mathematical algorithm called conditioned reconstruction (CR), it has been 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 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.

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Endosymbiosis in eukaryotes: 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.

More recent work proposes that gram-negative bacteria, which are unique within their domain in that they contain two lipid bilayer membranes, did result from an endosymbiotic fusion of archaeal and bacterial species. The double membrane would be a direct result of 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. A lot of skepticism still surrounds this hypothesis; the ideas are still debated within the biological science community.

There are several other competing hypotheses as to the origin of eukaryotes and the nucleus. One idea about how the eukaryotic nucleus evolved is that prokaryotic cells produced an additional membrane which 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. Another hypothesis, the nucleus-first hypothesis, proposes the nucleus evolved in prokaryotes first, followed by a later fusion of the new eukaryote with bacteria that became mitochondria. The mitochondria-first hypothesis, however, proposes mitochondria were first established in a prokaryotic host, which subsequently acquired a nucleus (by fusion or other mechanisms) to become the first eukaryotic cell. Most interestingly, the eukaryote-first hypothesis proposes prokaryotes actually evolved from eukaryotes by losing genes and complexity. All of these hypotheses are testable. Only time and more experimentation will determine which hypothesis is best supported by data.

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Three hypotheses of eukaryotic and prokaryotic evolution: 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, Network, and Ring of Life Models

To more accurately describe the phylogenetic relationships of life, web and ring models have been proposed as updates to tree models.

Learning Objectives

Describe the web, network, and ring of life models of phylogenetic trees

Key Takeaways

Key Points

  • A phylogenetic model that resembles a web or a network was proposed since eukaryotes evolved not from a single prokaryotic ancestor, but from a pool of many species that were sharing genes by HGT mechanisms.
  • A phylogenetic model that resembles a ring was proposed in which species of all three domains, Archaea, Bacteria, and Eukarya, evolved from a single pool of gene-swapping prokaryotes.
  • Phylogenetic models will continue to evolve as phylogeneticists remain highly skeptical of the current tree, web, and ring models.

Key Terms

  • web of life: a phylogenetic model that resembles a web or a network more than a tree
  • ring of life: a phylogenetic model where all three domains of life (Archaea, Bacteria, and Eukarya) evolved from a pool of primitive prokaryotes

The recognition of the importance of Horizontal gene transfer (HGT), especially in the evolution of prokaryotes, has caused some to propose abandoning the classic “tree of life” model. In 1999, a phylogenetic model that resembles a web or a network more than a tree was proposed. 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. Some individual prokaryotes were responsible for transferring the bacteria that caused mitochondrial development in 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 with its multiple trunks as a phylogenetic tree to represent the evolutionary role for HGT.

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Phylogenetic web of life model: 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.

Others have proposed abandoning any tree-like model of phylogeny in favor of a ring structure. The ” ring of life ” is a phylogenetic model where all three domains of life evolved from a pool of primitive prokaryotes. Using the conditioned reconstruction algorithm, it 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. This structure is proposed as the best fit for data from extensive DNA analyses; the ring model is the only one that adequately takes HGT and genomic fusion into account. However, phylogeneticists remain highly skeptical of this model.

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Phylogenetic ring of life model: 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. This does not 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 that time.