Information

6.2: Limitations of Phylogenetic Trees - Biology


Limitations of phylogenetic trees include the inability to distinguish evolutionary time and relatedness between distinct species.

Learning Objectives

  • Identify the limitations of phylogenetic trees as representations of the organization of life

Key Points

  • Closely-related species may not always look more alike, while groups that are not closely related yet evolved under similar conditions, may appear more similar to each other.
  • In phylogenetic trees, branches do not usually account for length of time and only depict evolutionary order.
  • Phylogenetic trees are like real trees in that they do not simply grow in only one direction after a new branch forms; the evolution of one organism does not necessarily signify the evolutionary end of another.

Key Terms

  • phenotypical: of or pertaining to a phenotype: the appearance of an organism based on a multifactorial combination of genetic traits and environmental factors

Limitations of Phylogenetic Trees

It may be easy to assume that more closely-related organisms look more alike; while this is often the case, it is not always true. If two closely-related lineages evolved under significantly varied surroundings or after the evolution of a major new adaptation, it is possible for the two groups to appear more different than other groups that are not as closely related. For example, the phylogenetic tree shows that lizards and rabbits both have amniotic eggs, whereas frogs do not; yet lizards and frogs appear more similar than lizards and rabbits.

Another aspect of phylogenetic trees is that, unless otherwise indicated, the branches do not account for length of time, only the evolutionary order. In other words, the length of a branch does not typically mean more time passed; nor does a short branch mean less time passed, unless specified on the diagram. A tree may not indicate how much time passed between the evolution of amniotic eggs and hair. What the tree does show is the order in which things took place. For example, the tree in the diagram shows that the oldest trait is the vertebral column, followed by hinged jaws, and so forth. Remember, any phylogenetic tree is a part of the greater whole and, as with a real tree, it does not grow in only one direction after a new branch develops. So, simply because a vertebral column evolved does not mean that invertebrate evolution ceased. It only means that a new branch formed. Also, groups that are not closely related, but evolve under similar conditions, may appear more phenotypically similar to each other than to a close relative.


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.

--> Test Prep for AP ® Courses

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    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.


    20.1 Organizing Life on Earth

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

    • Discuss the need for a comprehensive classification system
    • List the different levels of the taxonomic classification system
    • Describe how systematics and taxonomy relate to phylogeny
    • Discuss a phylogenetic tree's components and purpose

    In scientific terms, phylogeny is the evolutionary history and relationship of an organism or group of organisms. A phylogeny describes the organisim's relationships, such as from which organisms it may have evolved, or to which species it is most closely related. Phylogenetic relationships provide information on shared ancestry but not necessarily on how organisms are similar or different.

    Phylogenetic Trees

    Scientists use a tool called a phylogenetic tree to show the evolutionary pathways and connections among organisms. A phylogenetic tree is a diagram used to reflect evolutionary relationships among organisms or groups of organisms. Scientists consider phylogenetic trees to be a hypothesis of the evolutionary past since one cannot go back to confirm the proposed relationships. In other words, we can construct a “tree of life” to illustrate when different organisms evolved and to show the relationships among different organisms (Figure 20.2).

    Unlike a taxonomic classification diagram, we can read a phylogenetic tree like a map of evolutionary history. Many phylogenetic trees have a single lineage at the base representing a common ancestor. Scientists call such trees rooted , which means there is a single ancestral lineage (typically drawn from the bottom or left) to which all organisms represented in the diagram relate. Notice in the rooted phylogenetic tree that the three domains— Bacteria, Archaea, and Eukarya—diverge from a single point and branch off. The small branch that plants and animals (including humans) occupy in this diagram shows how recent and miniscule these groups are compared with other organisms. Unrooted trees do not show a common ancestor but do show relationships among species.

    In a rooted tree, the branching indicates evolutionary relationships (Figure 20.3). The point where a split occurs, a branch point , represents where a single lineage evolved into a distinct new one. We call a lineage that evolved early from the root that remains unbranched a basal taxon . We call two lineages stemming from the same branch point sister taxa . A branch with more than two lineages is a polytomy and serves to illustrate where scientists have not definitively determined all of the relationships. Note that although sister taxa and polytomy do share an ancestor, it does not mean that the groups of organisms split or evolved from each other. Organisms in two taxa may have split at a specific branch point, but neither taxon gave rise to the other.

    The diagrams above can serve as a pathway to understanding evolutionary history. We can trace the pathway from the origin of life to any individual species by navigating through the evolutionary branches between the two points. Also, by starting with a single species and tracing back towards the "trunk" of the tree, one can discover species' ancestors, as well as where lineages share a common ancestry. In addition, we can use the tree to study entire groups of organisms.

    Another point to mention on phylogenetic tree structure is that rotation at branch points does not change the information. For example, if a branch point rotated and the taxon order changed, this would not alter the information because each taxon's evolution from the branch point was independent of the other.

    Many disciplines within the study of biology contribute to understanding how past and present life evolved over time these disciplines together contribute to building, updating, and maintaining the “tree of life.” Systematics is the field that scientists use to organize and classify organisms based on evolutionary relationships. Researchers may use data from fossils, from studying the body part structures, or molecules that an organism uses, and DNA analysis. By combining data from many sources, scientists can construct an organism's phylogeny Since phylogenetic trees are hypotheses, they will continue to change as researchers discover new types of life and learn new information.

    Limitations of Phylogenetic Trees

    It may be easy to assume that more closely related organisms look more alike, and while this is often the case, it is not always true. If two closely related lineages evolved under significantly varied surroundings, it is possible for the two groups to appear more different than other groups that are not as closely related. For example, the phylogenetic tree in Figure 20.4 shows that lizards and rabbits both have amniotic eggs whereas, frogs do not. Yet lizards and frogs appear more similar than lizards and rabbits.

    Another aspect of phylogenetic trees is that, unless otherwise indicated, the branches do not account for length of time, only the evolutionary order. In other words, a branch's length does not typically mean more time passed, nor does a short branch mean less time passed— unless specified on the diagram. For example, in Figure 20.4, the tree does not indicate how much time passed between the evolution of amniotic eggs and hair. What the tree does show is the order in which things took place. Again using Figure 20.4, the tree shows that the oldest trait is the vertebral column, followed by hinged jaws, and so forth. Remember that any phylogenetic tree is a part of the greater whole, and like a real tree, it does not grow in only one direction after a new branch develops. Thus, for the organisms in Figure 20.4, just because a vertebral column evolved does not mean that invertebrate evolution ceased. It only means that a new branch formed. Also, groups that are not closely related, but evolve under similar conditions, may appear more phenotypically similar to each other than to a close relative.

    Link to Learning

    Head to this website to see interactive exercises that allow you to explore the evolutionary relationships among species.

    Classification Levels

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

    The taxonomic classification system (also called the Linnaean system after its inventor, Carl Linnaeus, a Swedish botanist, zoologist, and physician) uses a hierarchical model. Moving from the point of origin, the groups become more specific, until one branch ends as a single species. For example, after the common beginning of all life, scientists divide organisms into three large categories called domains: Bacteria, Archaea, and Eukarya. Within each domain is a second category called a kingdom . After kingdoms, the subsequent categories of increasing specificity are: phylum , class , order , family , genus , and species (Figure 20.5).

    The kingdom Animalia stems from the Eukarya domain. Figure 20.5 above shows the classification for the common dog. Therefore, the full name of an organism technically has eight terms. For the dog it is: Eukarya, Animalia, Chordata, Mammalia, Carnivora, Canidae, Canis, and lupus. Notice that each name is capitalized except for species, and the genus and species names are italicized. Scientists generally refer to an organism only by its genus and species, which is its two-word scientific name, or binomial nomenclature . Therefore, the scientific name of the dog is Canis lupus. The name at each level is also a taxon . In other words, dogs are in order Carnivora. Carnivora is the name of the taxon at the order level Canidae is the taxon at the family level, and so forth. Organisms also have a common name that people typically use, in this case, dog. Note that the dog is additionally a subspecies: the “familiaris” in Canis lupus familiaris. Subspecies are members of the same species that are capable of mating and reproducing viable offspring, but they are separate subspecies due to geographic or behavioral isolation or other factors.

    Figure 20.6 shows how the levels move toward specificity with other organisms. Notice how the dog shares a domain with the widest diversity of organisms, including plants and butterflies. At each sublevel, the organisms become more similar because they are more closely related. Historically, scientists classified organisms using characteristics, but as DNA technology developed, they have determined more precise phylogenies.

    Visual Connection

    At what levels are cats and dogs part of the same group?

    Link to Learning

    Visit this website to explore the classifications of thousands of organisms. This reference site contains about 10% of the described species on the planet.

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

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      Perspectives on the Phylogenetic Tree

      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 1a), which served as a pattern for subsequent studies for more than a century. The concept of a phylogenetic tree with a single trunk representing a common ancestor, with the branches representing the divergence of species from this ancestor, fits well with the structure of many common trees, such as the oak (Figure 1b). 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.

      Figure 1: The (a) concept of the “tree of life” goes back to an 1837 sketch by Charles Darwin. Like an (b) oak tree, the “tree of life” has a single trunk and many branches. (credit b: modification of work by “Amada44″/Wikimedia Commons. “tree of life” by OpenStax is licensed under CC BY 4.0)

      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 1).

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

      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 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 2). 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 such as carrots, apricots, mangoes, and sweet potatoes. On the other hand, aphids have acquired the ability to make carotenoids on their own. According to DNA analysis, this ability is due to the transfer of fungal genes into the insect by HGT, presumably as the insect consumed fungi for food. A carotenoid enzyme called a desaturase is responsible for the red coloration seen in certain aphids, and it has been further shown that when this gene is inactivated by mutation, the aphids revert back to their more common green color (Figure 2).

      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 genes for making carotenoids are inactivated by mutation, the aphids revert back to (b) their green color. Red coloration makes the aphids a lot more conspicuous to predators, but evidence suggests that red aphids are more resistant to insecticides than green ones. Thus, red aphids may be more fit to survive in some environments than green ones. (credit a: modification of work by Benny Mazur credit b: modification of work by Mick Talbot. “aphids” by OpenStax is licensed under CC BY 4.0)

      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 3a). 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 3b) proposes that gram-negative bacteria, which are unique within their domain in that they contain two lipid bilayer membranes, indeed resulted from an endosymbiotic fusion of archaeal and bacterial species. The double membrane would be a direct result of the endosymbiosis, with the endosymbiont picking up the second membrane from the host as it was internalized. This mechanism has also been used to explain the double membranes found in mitochondria and chloroplasts. Lake’s work is not without skepticism, and the ideas are still debated within the biological science community. In addition to Lake’s hypothesis, there are several other competing theories as to the origin of eukaryotes. How did the eukaryotic nucleus evolve? One theory is that the prokaryotic cells produced an additional membrane that surrounded the bacterial chromosome. Some bacteria have the DNA enclosed by two membranes however, there is no evidence of a nucleolus or nuclear pores. Other proteobacteria also have membrane-bound chromosomes. If the eukaryotic nucleus evolved this way, we would expect one of the two types of prokaryotes to be more closely related to eukaryotes.

      Figure 3: 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. (credit: “endosymbiosis” by OpenStax is licensed under CC BY 4.0)

      The nucleus-first hypothesis proposes that the nucleus evolved in prokaryotes first (Figure 4a), 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 4b), which subsequently acquired a nucleus, by fusion or other mechanisms, to become the first eukaryotic cell. The eukaryote-first hypothesis proposes that prokaryotes actually evolved from eukaryotes by losing genes and complexity (Figure 4c). All of these hypotheses are testable. Only time and more experimentation will determine which hypothesis is best supported by data.

      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. (credit: “Three alternate hypotheses” by OpenStax is licensed under CC BY 4.0)

      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. (credit b: modification of work by “psyberartist”/Flickr. “Doolittle, the “tree of life”” by OpenStax is licensed under CC BY 4.0)

      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 6) 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. (credit: “ring of life” by OpenStax is licensed under CC BY 4.0)

      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.

      Summary

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


      Seeing the Forest for the Trees: The Limitations of Phylogenies in Comparative Biology (American Society of Naturalists Address) *

      The past 30 years have seen a revolution in comparative biology. Before that time, systematics was not at the forefront of the biological sciences, and few scientists considered phylogenetic relationships when investigating evolutionary questions. By contrast, systematic biology is now one of the most vigorous disciplines in biology, and the use of phylogenies not only is requisite in macroevolutionary studies but also has been applied to a wide range of topics and fields that no one could possibly have envisioned 30 years ago. My message is simple: phylogenies are fundamental to comparative biology, but they are not the be-all and end-all. Phylogenies are powerful tools for understanding the past, but like any tool, they have their limitations. In addition, phylogenies are much more informative about pattern than they are about process. The best way to fully understand the past—both pattern and process—is to integrate phylogenies with other types of historical data as well as with direct studies of evolutionary process.


      Phylogenetic tree

      A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the inferred evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical and/or genetic characteristics. The taxa joined together in the tree are implied to have descended from a common ancestor. In a rooted phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of the descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units (HTUs) as they cannot be directly observed. Trees are useful in fields of biology such as systematics and comparative phylogenetics.

      A speculatively rooted tree for rRNA genes

      The idea of a "tree of life" arose from ancient notions of a ladder-like progression from lower to higher forms of life (such as in the Great Chain of Being). Early representations of branching phylogenetic trees include a "Paleontological chart" showing the geological relationships among plants and animals in the book Elementary Geology, by Edward Hitchcock (first edition: 1840).

      Charles Darwin (1859) also produced one of the first illustrations and crucially popularized the notion of an evolutionary "tree" in his seminal book The Origin of Species. Over a century later, evolutionary biologists still use tree diagrams to depict evolution because such diagrams effectively convey the concept that speciation occurs through the adaptive and random splitting of lineages. Over time, species classification has become less static and more dynamic.

      Fig. 1: Unrooted tree of the myosin supergene family[1] (*)


      Fig. 2: A highly resolved, automatically generated Tree Of Life, based on completely sequenced genomes [2][3].

      A phylogenetic tree, showing how Eukaryota and Archaea are more closely related to each other than to Bacteria, based on Cavalier-Smith's theory of bacterial evolution. (Cf. LUCA, Neomura.)

      A rooted phylogenetic tree is a directed tree with a unique node corresponding to the (usually imputed) most recent common ancestor of all the entities at the leaves of the tree. The most common method for rooting trees is the use of an uncontroversial outgroup — close enough to allow inference from sequence or trait data, but far enough to be a clear outgroup.

      Unrooted trees illustrate the relatedness of the leaf nodes without making assumptions about ancestry at all. While unrooted trees can always be generated from rooted ones by simply omitting the root, a root cannot be inferred from an unrooted tree without some means of identifying ancestry this is normally done by including an outgroup in the input data or introducing additional assumptions about the relative rates of evolution on each branch, such as an application of the molecular clock hypothesis. Figure 1 depicts an unrooted phylogenetic tree for myosin, a superfamily of proteins.[4]

      Both rooted and unrooted phylogenetic trees can be either bifurcating or multifurcating, and either labeled or unlabeled. A rooted bifurcating tree has exactly two descendants arising from each interior node (that is, it forms a binary tree), and an unrooted bifurcating tree takes the form of an unrooted binary tree, a free tree with exactly three neighbors at each internal node. In contrast, a rooted multifurcating tree may have more than two children at some nodes and an unrooted multifurcating tree may have more than three neighbors at some nodes. A labeled tree has specific values assigned to its leaves, while an unlabeled tree, sometimes called a tree shape, defines a topology only. The number of possible trees for a given number of leaf nodes depends on the specific type of tree, but there are always more multifurcating than bifurcating trees, more labeled than unlabeled trees, and more rooted than unrooted trees. The last distinction is the most biologically relevant it arises because there are many places on an unrooted tree to put the root. For labeled bifurcating trees, there are

      (2n-3)!! = (2n-3)! /2 ( n-2) (n-2)! for n >= 2

      (2n-5)!! = (2n-5)! / 2^ (n-3) (n-3)! for n >= 3

      total unrooted trees, where n represents the number of leaf nodes. Among labeled bifurcating trees, the number of unrooted trees with n leaves is equal to the number of rooted trees with n − 1 leaves.[5]

      A dendrogram is a broad term for the diagrammatic representation of a phylogenetic tree.

      A cladogram is a tree formed using cladistic methods. This type of tree only represents a branching pattern, i.e., its branch lengths do not represent time.

      A phylogram is a phylogenetic tree that explicitly represents number of character changes through its branch lengths.

      A chronogram is a phylogenetic tree that explicitly represents evolutionary time through its branch lengths.

      Construction
      Main article: Computational phylogenetics

      Phylogenetic trees among a nontrivial number of input sequences are constructed using computational phylogenetics methods. Distance-matrix methods such as neighbor-joining or UPGMA, which calculate genetic distance from multiple sequence alignments, are simplest to implement, but do not invoke an evolutionary model. Many sequence alignment methods such as ClustalW also create trees by using the simpler algorithms (i.e. those based on distance) of tree construction. Maximum parsimony is another simple method of estimating phylogenetic trees, but implies an implicit model of evolution (i.e. parsimony). More advanced methods use the optimality criterion of maximum likelihood, often within a Bayesian Framework, and apply an explicit model of evolution to phylogenetic tree estimation.[5] Identifying the optimal tree using many of these techniques is NP-hard[5], so heuristic search and optimization methods are used in combination with tree-scoring functions to identify a reasonably good tree that fits the data.

      Tree-building methods can be assessed on the basis of several criteria:[6]

      * efficiency (how long does it take to compute the answer, how much memory does it need?)
      * power (does it make good use of the data, or is information being wasted?)
      * consistency (will it converge on the same answer repeatedly, if each time given different data for the same model problem?)
      * robustness (does it cope well with violations of the assumptions of the underlying model?)
      * falsifiability (does it alert us when it is not good to use, i.e. when assumptions are violated?)

      Tree-building techniques have also gained the attention of mathematicians. Trees can also be built using T-theory.[7]

      Although phylogenetic trees produced on the basis of sequenced genes or genomic data in different species can provide evolutionary insight, they have important limitations. They do not necessarily accurately represent the species evolutionary history. The data on which they are based is noisy the analysis can be confounded by horizontal gene transfer[8], hybridisation between species that were not nearest neighbors on the tree before hybridisation takes place, convergent evolution, and conserved sequences.

      Also, there are problems in basing the analysis on a single type of character, such as a single gene or protein or only on morphological analysis, because such trees constructed from another unrelated data source often differ from the first, and therefore great care is needed in inferring phylogenetic relationships among species. This is most true of genetic material that is subject to lateral gene transfer and recombination, where different haplotype blocks can have different histories. In general, the output tree of a phylogenetic analysis is an estimate of the character's phylogeny (i.e. a gene tree) and not the phylogeny of the taxa (i.e. species tree) from which these characters were sampled, though ideally, both should be very close. For this reason, serious phylogenetic studies generally use a combination of genes that come from different genomic sources (e.g., from mitochondrial or plastid vs. nuclear genomes), or genes that would be expected to evolve under different selective regimes, so that homoplasy (false homology) would be unlikely to result from natural selection.

      When extinct species are included in a tree, they are terminal nodes, as it is unlikely that they are direct ancestors of any extant species. Scepticism must apply when extinct species are included in trees that are wholly or partly based on DNA sequence data, due to the fact that little useful "ancient DNA" is preserved for longer than 100,000 years, and except in the most unusual circumstances no DNA sequences long enough for use in phylogenetic analyses have yet been recovered from material over 1 million years old.

      In some organisms, endosymbionts have an independent genetic history from the host.[9]

      Phylogenetic networks are used when bifurcating trees are not suitable, due to these complications which suggest a more reticulate evolutionary history of the organisms sampled.

      * Evolutionary history of life - An overview of the major time periods of life on earth
      * Life -
      * Three-domain system (cell types)

      * Archaeopteryx
      * Cladistics
      * Comparative phylogenetics
      * Computational phylogenetics
      * Evolutionary biology
      * Phylogenetics

      1. ^ Hodge T, Cope M (1 October 2000). "A myosin family tree". J Cell Sci 113 Pt 19 (19): 3353–4. PMID 10984423. http://jcs.biologists.org/cgi/content/full/113/19/3353.
      2. ^ Letunic, I Bork, P (2007). "Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation." (Pubmed). Bioinformatics 23(1) (1): 127–8. doi:10.1093/bioinformatics/btl529. PMID 17050570.
      3. ^ Ciccarelli, FD Doerks, T Von Mering, C Creevey, CJ Snel, B Bork, P (2006). "Toward automatic reconstruction of a highly resolved tree of life." (Pubmed). Science 311(5765) (5765): 1283–7. doi:10.1126/science.1123061. PMID 16513982.
      4. ^ Maher BA (2002). "Uprooting the Tree of Life". The Scientist 16: 18. http://www.the-scientist.com/yr2002/sep/research1_020916.html.
      5. ^ a b c Felsenstein J. (2004). Inferring Phylogenies Sinauer Associates: Sunderland, MA.
      6. ^ Penny, D., Hendy, M. D. & M. A. Steel. 1992. Progress with methods for constructing evolutionary trees. Trends in Ecology and Evolution 7: 73-79.
      7. ^ A. Dress, K. T. Huber, and V. Moulton. 2001. Metric Spaces in Pure and Applied Mathematics. Documenta Mathematica LSU 2001: 121-139
      8. ^ Woese C (2002). "On the evolution of cells". Proc Natl Acad Sci USA 99 (13): 8742–7. doi:10.1073/pnas.132266999. PMID 12077305.
      9. ^ Villarreal, L.P., & Witzany, G. (2010). Viruses are Essential Agents within the Roots and Stem of the Tree of Life. Journal of Theoretical Biology 262: 698-710.

      * Schuh, R. T. and A. V. Z. Brower. 2009. Biological Systematics: principles and applications (2nd edn.) ISBN 978-0-8014-4799-0

      * Phylogenetic Trees Based on 16s rDNA
      * Poster-sized tree of life illustration
      * A 3D View
      * Human Y-Chromosome 2002 Phylogenetic Tree
      * In 2003, the Science journal dedicated a special issue to the tree of life, including an online version of a tree of life.
      * iTOL: Interactive Tree Of Life
      * Phylogenetic Tree of Artificial Organisms Evolved on Computers


      Results

      Phylogeny and diversification

      All data and results, including the tree topology with support values (Appendix S1), are available in the SI text and DataDryad (https://datadryad.org/review?doi=doi:10.5061/dryad.h19t7b2). Our phylogeny is robust overall, with monophyly of all families, subfamilies, and genera strongly supported. Of particular note is the continued weak support for relationships in the tortoise family Testudinidae (but see [50]), as well as broader uncertainty in higher-level relationships among and placement of Cheloniidae, Chelydridae, Emydidae, and Platysternidae [47, 51,52,53].

      We recover a unique topology from these previous four analyses, with successive divergences of Chelydridae+Dermatemydidae+Kinosternidae, Cheloniidae+Dermochelyidae, Platysternidae, Emydidae, and Testudinidae+Geoemydidae [54]. This is based on the same or similar underlying datasets and may reflect issues such as mito-nuclear discordance and phylogenetic signal in the available loci. However, our increase in both taxon and characters sampling may indicate convergence on a more robust topology. Future analyses sampling more loci may be able to resolve these relationships with greater support.

      Several turtle clades have been identified by previous authors [18, 19, 51] as representing extraordinary instances of evolutionary diversification, including Galapagos tortoises (Chelonoidis), and New World emydids (Deirochelyinae). Similar results were recovered in our preliminary analyses. However, we believe strongly that these are artifactual, and represent an inconsistent application of species concepts and delimitation in turtles. At the current juncture, we are constrained by existing taxonomic frameworks, and these issues must thus be left to future studies. However, interpretation of our downstream results (see below) should be colored by knowledge of these issues. We attempt, when possible, to use analyses and interpret models in a way that is resilient to the possibility of low-level taxonomic biases.

      Results for turtles and crocodilians showed roughly constant rates of speciation and extinction, with no support for any shifts therein, or any global mass-extinction events (Fig. 1a). Turtles exhibit speciation rates of

      0.07 lineages per million years and extinction rates of

      0.03–0.04, for net diversification of

      0.03–0.04 and turnover probabilities of

      43–57% from the Jurassic to the present. For crocodilians, rates are

      0.02 respectively, for net diversification of

      40% from the Cretaceous to the present.

      Results from (a) TESS/CoMET analysis showing estimated speciation and extinction rates for turtles and crocodilians across time and (b) location of significant jumps (red) inferred under a Lévy process in crocodilians, Carettochelys, and three other species

      For body size, few strongly supported jumps are estimated by the model for branches subtending extant taxa (Fig. 1b). Thus, most variation can be attributed to steady drift over time for living species, in contrast to ecomorphologically diverse fossil relatives [16, 17]. One jump occurs along the stem branch leading to crocodilians, reflecting the difference in body size between the two groups, crocodilians being longer and heavier on average. A second occurs in the relict species Carettochelys insculpta, a large freshwater species, which is the sister lineage of the radiation of softshell turtles (Cyclanorbinae and Trionychinae) that contains both large and medium sized species. Three terminal species are also estimated as jumps, each of which is significantly smaller than its congeners. These are Pelodiscus parviformis, Pseudemys gorzugi, and Trachemys adiutrix. As noted above, these radiations have questionable species boundaries [55,56,57], and we refrain from interpreting these results further.

      ED and threat status

      We find a bi-modal distribution of ED values for extant turtles (Fig. 2). The primary mode is 17 Ma, older than amphibians at 16.5 Ma [31], squamate reptiles at 11 Ma [46], birds at 6.2 Ma [26, 28], or mammals at 4.8 Ma [58]. A secondary mode at 5 Ma is dominated by the recent “radiations” in Deirochelyinae and Testudininae (see Discussion), for which multi-locus nuclear datasets generally do not support the higher number of morphologically delimited lineages. Thus, we refrain from examining among-lineage rate variation for speciation or extinction.

      Randomly-selected phylogeny, with branches colored proportional to ED for extant lineages. The internal contrasting rings denote 50 Ma intervals. The insets show the overall distribution of ED across 356 turtle and 27 crocodilian species, and the distribution of ED across threat statuses, including both assessed and imputed species. Silhouettes are from http://ww.phylopic.org/ see Supplemental Information for license details

      Across the three methods for threat-status imputation, the final predictions for the 114 species are fairly similar (Appendix S5), with all models identifying area as the single-most important variable by far (Figs. S7–13), as in amphibians [20], birds [59], mammals [60], and squamate reptiles [24]. Each method picked out slightly different contributions from secondary predictors. The second-ranked variable for the PGLM model was occurrence in the Oriental ecoregion for the RF model there is a tie between AET (ecology) and HEI (anthropogenic disturbance) and for the ANN model it was spatial dissimilarity, indicating the geographic clustering of threat status (see below). Body size (length or mass) were not particularly important, unlike for amphibians [20], birds [21], mammals [22, 23], and some squamates [24, 61]. Training accuracy for the three models was higher (PGLM = 38%, RF = 49%, ANN = 48%) than random (17%) and confusion matrices showed high sensitivity and specificity (up to 86%), with errors usually involving only a single step in either direction.

      Overall, 21 species were predicted identically by all three approaches, and 69 agreed for two out of the three, for

      79% concordance overall. On a pairwise basis for 342 comparisons (114 species times three models), 141 were identical (41%) and an additional 144 (42%) were adjacent (one category different), for a total of 83% identical or adjacent predictions. Given the high level of agreement and lack of apparent bias towards higher or lower categories for any model, we simply used the mean of the three predictions for our final estimate of threat status.

      Our final estimate included 17 species classified as LC, 27 NT, 47 VU, 15 EN, and 8 CR. Imputed statuses showed a similar distribution of ED to known species (Fig. S14). Qualitatively, the imputed species were heavily concentrated in tropical pleurodiran lineages, particularly those with many recently described or resurrected species such as Pelusios [62] and Pelomedusa [63]. Nearly all of the primarily sub-Saharan African pelomedusines, and

      2/3 of the primarily Australasian chelodinines were imputed. No other subfamily with more than 2 species had fewer than 50% assessments. The final breakdown of assessed + imputed threat statuses used for subsequent analyses was 71 LC, 61 NT, 119 VU, 63 EN, 61 CR, and 9 EX. Thus, 66% of modern turtle and crocodilian species are threatened or extinct.

      Comparing ED across threat statuses (Fig. 3), non-threatened species (LC, NT) have significantly lower median ED (18 Ma vs. 21 Ma) than threatened species (VU, EN, CR), using a two-sample t-test (t = − 2.2, P = 0.03). This is driven primarily by the higher median ED of VU and CR taxa, while EN covers a broad range of high- and low-ED species (Fig. 2). Thus, imminent extinction of threatened species would represent a disproportionate loss of total evolutionary history across crocodilians and turtles, preferentially removing unique and derived lineages from the Tree of Life, indicating their more-precarious stature in the conservation landscape compared to other terrestrial vertebrates such as amphibians.

      Randomly-selected phylogeny, with branches colored according to threat status for all species imputed statuses are indicated with a tip marker. The internal contrasting rings denote 50 Ma intervals. The insets show the overall distribution of threat statuses (assessed are solid and imputed are transparent), and the distribution of ED across threatened vs. non-threatened, including both assessed and imputed species

      Combining the ED and threat statuses to calculate EDGE scores indicating the intersection of distinctiveness and risk, we highlight the top-10 at-risk turtles and crocodilians (Fig. 4 Table S1). These data also indicate that the highest-ranked turtles exceed crocodilians in their combination of ED and threat. We find that our estimated ED scores are similar to those from [4] when estimated directly from their phylogenetic dataset, but that a large cluster of their imputed values appear to be inflated (Fig. S15). Estimated EDGE scores are more similar between the two datasets, but variation in ED led previous authors to overemphasize some taxa (such as sea turtles Cheloninae) and underemphasize others (such as flapshell turtles Cyclanorbinae). Our dataset thus provides a more robust and presumably more accurate picture of ED and EDGE in the group (see Table S1).

      Boxplot of the top-100 ED turtles (a) and all crocodilians (b) with imputed statuses in bold, and insets showing boxplots of the top-10 EDGE species from both groups (c) and the divergence between ED (green) and EDGE (red) scores on a log scale (d). If all threat statuses were LC, ED and EDGE would be equal and the histograms would be identical. Their divergence thus shows the impact of extinction risk

      Geography of threat

      Geographically, threatened taxa are concentrated in a few major sub-areas [38] of the 11 global ecoregions [47]. The highest diversity of threatened species occurs in South and Southeast Asia in the Red, Mekong, Irawaddy, and Ganges-Brahmaputra River deltas and Peninsular Malaysia (Fig. 5a). Secondary hotspots occur in tropical western Africa, and the eastern Amazon River basin. In contrast, "arks" of non-threatened species are observed in the eastern Nearctic, Australia-New Guinea, eastern Africa, and the western Amazon River basin (Fig. 5b). We note that the prominence of the eastern Nearctic is reduced when species richness is weighted by EDGE scores (Fig. S4), accounting for the low distinctiveness of the high number of questionably delimited deirochelyine species in that area. Interestingly, there are also modest concentrations of non-threatened species (

      5–10) in the Ganges-Brahmaputra River delta and the Yucatan peninsula, both regions characterized by several high-ED threatened species (Figs. 4 and 5). Finally, island endemicity is not a strong predictor of threat status from any of the models, and regions such as Madagascar and the Philippines that have flagship high-ED threatened species (Table S1) nevertheless don’t represent concentrated hotspots of threat.

      Spatial richness map showing distribution of species assessed or predicted to be threatened (a) or non-threatened (b). Note threat hotspots in the eastern Amazon, west Africa, south Asia, and southeast Asia compared to relative havens in the eastern Nearctic, western Amazon, eastern Africa, and northern Australia. Maps were created by RAP using the WGS84 datum, in R version 3.6.3, in the package 'sf' version 0.9–3


      Free Response

      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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