Module 9 Quiz

Explain the hierarchy of groupings in taxonomy.

1) Domain 2) Kingdom 3) Phylum 4) Class 5) Order 6) Family 7) Genus 8) Species Why is it useful to categorize species into groups? The three domains of life contain millions of different species. Subdividing them into progressively smaller taxonomic groups makes it easier for biologists to appreciate the relationships among such a large number of species. Below the domain and the supergroup is the kingdom, which is divided into phyla (singular, phylum). Each phylum is divided into classes, then orders, families, genera (singular, genus) and species. As noted in Chapter 25, species may be divided into subspecies, often based on geographical distribution. Each of these taxa contains progressively fewer species that are more similar to each other than they are to the members of the taxa above them in the hierarchy. For example, the taxon Animalia, which is at the kingdom level, has a larger number of fairly diverse species than does the class Mammalia, which contains fewer species that are relatively similar to each other. To further understand taxonomy, let's consider the classification of the gray wolf (Canis lupus). The gray wolf is placed in the domain Eukarya, the supergroup Opisthokonta, and then within the kingdom Animalia. This kingdom contains all animals and has over 1 million species. Next, the gray wolf is classified in the phylum Chordata. The 50,000 species of animals in this phylum all have four common features at some stage of their development. These are a notochord (a cartilaginous rod that runs along the back of all chordates at some point in their life cycle), a tubular nerve or spinal cord located above the notochord, gill slits or arches, and a postanal tail. Examples of animals in the phylum Chordata include fishes, reptiles, and mammals. The gray wolf is in the class Mammalia, which includes 5,513 species of mammals. Two distinguishing features of animals in this class are hair, which helps the body maintain a warm, constant body temperature, and mammary glands, which produce milk to nourish the young. There are 26 orders of mammals the order that includes the gray wolf is called Carnivora and has 282 species that are meat-eating animals with prominent canine teeth. The gray wolf is placed in the family Canidae, which is a relatively small family of 24 species, including different species of wolves, jackals, foxes, wild dogs, and the coyote and domestic dog. All species in the family Canidae are doglike animals. The smallest grouping that contains the gray wolf is the genus Canis, which has four species of jackals the coyote, and two types of wolves. The species Canis lupus encompasses several subspecies, including the domestic dog (Canis lupus familiaris). The domain Eukarya formerly consisted of four kingdoms called Protista, Fungi, Plantae, and Animalia. However, researchers later discovered that protists do not constitute a separate kingdom but instead are a very broad collection of species. Taxonomists now place most eukaryotes into seven groups called supergroups. In the taxonomy of eukaryotes, a supergroup lies between a domain and a kingdom. As discussed in Chapter 28, all seven supergroups contain a distinctive group of protists. In addition, kingdoms Fungi and Animalia are within the supergroup Opisthokonta, because they are closely related to the protists in this supergroup. Kingdom Plantae is within the supergroup called Land plants and relatives. Plants are closely related to green algae, which are protists in this supergroup.

Differentiate between an ingroup and outgroup in a cladistical analysis

A Cladistics Approach Produces a Cladogram Based on Shared Derived Characters To show how shared derived characters are used to propose a phylogenetic tree, figure 26.9a compares several traits among five species of animals. The proposed cladogram in Figure 26.9b is consistent with the distribution of shared derived characters among these species. A branch point is where two species differ in a character. The oldest common ancestor, which is now extinct, had a notochord and was an ancestor to all five species. Vertebrae are a shared derived character of the lamprey, salmon, lizard, and rabbit, but not the lancelet, which is an invertebrate. By comparison, a hinged jaw is a shared derived character of the salmon, lizard, and rabbit, but not of the lamprey or lancelet. ***In a cladogram, an ingroup is the group whose evolutionary relationships we wish to understand. ***By comparison, an outgroup is a species or group of species that is assumed to have diverged before the species in the ingroup.An outgroup lacks one or more shared derived characters that are found in the ingroup. A designated outgroup can be closely related or more distantly related to the ingroup. In the tree shown in Figure 26.9, if the salmon, lizard, and rabbit are an ingroup, the lamprey is an outgroup. The lamprey has a notochord and vertebrate but lacks a character shared by the ingroup, namely, a hinged jaw. Thus, for the ingroup, the notochord and vertebrate are shared primitive characters, whereas the hinged jaw is a shared derived character not found in the outgroup.

Be able to identify on a phylogeny a monophyletic group, a paraphyletic group, and a polyphyletic group

Look at example on top of page 152

Differentiate between a node and a clade

****The branch points in a phylogenetic tree, also called nodes, indicate times when cladogenesis has occurred. The branch points of a phylogenetic tree group species according to common ancestry. ****A clade consists of a common ancestral species and all of its descendant species. Likewise, the entire tree forms a clade, with species A as a common ancestor. Therefore, smaller and more recent clades are nested within larger clades that have older common ancestors.

Differentiate between homologous traits and analogous traits

As discussed in Chapter 23, the term homology refers to a similarity that occurs due to descent from a common ancestor. Such features are said to be homologous. For example, the arm of a human, the wing of a bat, and the flipper of a whale are homologous structures (refer back to Figure 23.12). Similarly, genes found in different species are homologous if they have been derived from the same ancestral gene (refer back to Figure 23.13). In systematics, researchers identify homologous features that are shared by some species but not by others, which allows them to group species based on shared similarities. Researchers usually study homology by examining morphological features or genetic data. In addition, the data they gather are viewed in light of geographic data. Many organisms do not migrate extremely long distances. Species that are closely related evolutionarily are relatively likely to inhabit neighboring or overlapping geographic regions, though many exceptions are known to occur. Vertebrate forelimbs are used for flight (birds and bats), orientation during swimming (whales and seals), running (horses), climbing (arboreal lizards), and swinging from tree branches (monkeys). Howeve,r all vertebrate forelimbs contain the same sets of bones organized in similar ways, despite their dissimilar funcitons. The most plausible explanation for this unit of anatomy is that the basic forelimb plan belonged to a common ancestor, and then the plan became modified in the succeeding groups as each continued along its own evolutionary pathway. Anatomically similar structures explainable by inheritance from a common ancestor are called homologous structures. In contrast, analogous structures serve the same function but are not constructed similarly, and therefore could not have a common ancestry. The wings of birds and insects are analogous structures.

Describe how species are named using binomial nomenclature

As originally advocated by Linnaeus, binomial nomenclature is the standard method for naming species. The scientific name of every species has two names, its genus name and its unique specific epithet. For the gray wolf, the genus is Canis and the species epithet is lupus. The genus name is always capitalized, but the specific epithet is not. Both names are italicized. After the first mention, the genus name is abbreviated to a single letter. For example, we write that Canis lupus is the gray wolf, and in subsequent sentences, the species is referred to as C. lupus. When naming a new species, genus names are always nouns or treated as nouns, whereas species epithets may be either nouns or adjectives. The names often have a Latin or Greek origin and refer to characteristics of the species or to features of its habitat. For example, the genus name of the newly discovered African forest elephant, Loxodonta, is from the Greek loxo, meaning slanting, and odonta, meaning tooth. The species epithet cyclotis refers to the observation that the ears of this species are rounder than those of L. africana. The rules for naming animal species, such as Canis lupus and Loxodonta africana, were established by the International Commission on Zoological Nomenclature (ICZN). The ICZN provides and regulates a uniform system of nomenclature to ensure that every animal has a unique and universally accepted scientific name. Who is allowed to identify and name a new species? As long as ICZN rules are followed, new animal species can be named by anyone, not only scientists. The rules for naming plants are described in the International Code of Botanical Nomenclature (ICBN), and the naming of bacteria and archaea is overseen by the International Committee on Systematics of Prokaryotes (ICSP).

Describe why constructing monophyletic groups is the goal of systematics.

Because the grouping of a taxon needs to include a common ancestor and all of the descendants of that common ancestor. A monophyletic group is group of organisms classified in the same taxon. A taxon that is a clade (a clade includes a common ancestor and all of the descendants of that common ancestor). Ideally, every taxon, whether it is a domain, supergroup, kingdom, phylum, class, order, family, or genus, should be a monophyletic group.

Describe the role cladograms play in cladistics

Cladograms are a visual organization, a way we represent ancestral and derived characters so that it is easy for us to follow. Cladogram starts with ancestral trait and works its way up to more and more derived characters. Cladistics is the classification of species based on evolutionary relationships. A cladistics approach produces phylogenetic trees by considering the possible pathways of evolutionary change that involve characteristics that are shared or not shared among various species. Such trees are known as cladograms. In this section, we will consider how biologists produce phylogenetic trees. Species Differ with Regard to Primitive and Derived Characters. A cladistics approach compares homologous features, also called characters, which may exist in two or more character states. For example, among different species, a front limb, which is a character, may exist in different character states such as a wing, an arm, or a flipper. The various character states are either shared or not shared by different species. To understand the cladistics approach, let's take a look at a simplified phylogeny (figure 26.8). We can place the species that currently exist into two groups: D and E, and F and G. The most recent common ancestor to D and E is B, whereas species C is the most recent common ancestor to F and G. With these ideas in mind, let's focus on the front limbs (flippers versus legs) and eyes. ****A character trait that is shared by two or more different taxa and inherited from ancestors older than their last common ancestor is called a shared primitive character, or symplesiomorphy. Such characters are viewed as being older—ones that occurred earlier in evolution. With regard to species D, E, F, and G, having two eyes is a shared primitive character. It originated prior to species B and C. ****By comparison, a shared derived character, or synapomorphy, is a character that is shared by two or more species or taxa and has originated in their most recent common ancestor. With regard to species D and E, having two front flippers is a shared derived character that originated in species B, their most recent common ancestor (see figure 26.8). Compared with shared primitive characters, shared derived characters are more recent traits on an evolutionary timescale. For example, among mammals, only some species, such as whales and dolphins, have flippers. In this case, flippers were derived from the two front limbs of an ancestral species. The word derived indicates that evolution involves the modification of traits in pre-existing species. In other words, populations of organisms with new traits are derived from changes in pre-existing populations. The basics of the cladistic approach is to analyze many shared derived characters among groups of species to deduce the pathway that gave rise to those species. Note that the terms primitive and derived do not indicate the complexity of a character. For example, the flippers of a dolphin do not appear more complex than the front limbs of ancestral species A, which were limbs with individual toes. Derived characters can be similar in complexity, less complex, or more complex than primitive characters. A Cladistics Approach Produces a Cladogram Based on Shared Derived Characters To show how shared derived characters are used to propose a phylogenetic tree, figure 26.9a compares several traits among five species of animals. The proposed cladogram in Figure 26.9b is consistent with the distribution of shared derived characters among these species. A branch point is where two species differ in a character. The oldest common ancestor, which is now extinct, had a notochord and was an ancestor to all five species. Vertebrae are a shared derived character of the lamprey, salmon, lizard, and rabbit, but not the lancelet, which is an invertebrate. By comparison, a hinged jaw is a shared derived character of the salmon, lizard, and rabbit, but not of the lamprey or lancelet. ****In a cladogram, an ingroup is the group whose evolutionary relationships we wish to understand. By comparison, an outgroup is a species or group of species that is assumed to have diverged before the species in the ingroup. An ourgroup lacks one or more shared derived characters that are found in the ingroup. A designated outgroup can be closely related or more distantly related to the ingroup. In the tree shown in Figure 26.9, if the salmon, lizard, and rabbit are an ingroup, the lamprey is an outgroup. The lamprey has a notochord and vertebrate but lacks a character shared by the ingroup, namely, a hinged jaw. Thus, for the ingroup, the notochord and vertebrate are shared primitive characters, whereas the hinged jaw is a shared derived character not found in the outgroup. Likewise, the concept of shared derived characters can apply to molecular data, such as a gene sequence. (LOOK AT FIGURE 26.10) Now that we have an understanding of shared primitive and derived characters, let's consider the steps a researcher would follow to propose a cladogram using a cladistics approach. 1) Choose the species whose evolutionary relationships are of interest. In a simple cladogram, such as those described in this chapter, individual species are compared with each other. In more complex cladograms, species may be grouped into larger taxa (for example, families) and compared with each other. If such grouping is done, the results are not reliable if the groups are not clades. 2) Choose characters for comparing the species selected in step 1. As mentioned, a character is a general feature of an organism and may come in different versions called character states. For example, a front limb is a character in mammals, which could exist in different character states such as a wing, an arm, or a flipper. 3) Determine the polarity of character states. In other words, determine if a character state came first and is primitive or came later and is a derived character. This information may be available by examining the fossil record, for example, but is usually done by comparing the ingroup with the outgroup. For a character with two character states, an assumption is made that a character state shared by the outgroup and ingroup is primitive. A character state shared only by members of the ingroup is derived. 4) Analyze cladograms based on the following principles: a. All species (or higher taxa) are placed on tips in a phylogenetic tree, not at branch points b. Each cladogram branch point should have a list of one or more shared derived characters that are common to all species above the branch point unless the character is later modified c. All shared derived characters appear together only once in a cladogram unless they arose independently during evolution more than once. 5) Among many possible options, choose the cladogram that provides the simplest explanation for the data. A common approach is to use a computer program that generates many possible cladograms. Analyzing the data and choosing among the possibilities are key aspects of this process. As described later, different theoretical approaches, such as the principle of parsimony, can be used to choose among possible phylogenies. 6) Provide a root to the phylogenetic tree by choosing a noncontroversial outgroup. In this textbook, most phylogenetic trees are rooted, which means that a single node at the bottom of the tree corresponds to a common ancestor for all of the species or groups of species in the tree. A method for rooting trees is the use of a noncontroversial outgroup. Such an outgroup typically shares morphological traits and/or DNA sequence similarities with the members of the ingroup, to allow a comparison between the ingroup and outgroup. Even so, the outgroup must be non-controversial in that it has enough distinctive differences with the ingroup to be considered a clear outgroup. For example, if the ingroup was a group of mammalian species, an outgroup could be a reptile.

Describe how DNA sequences can be used in molecular systematics

Molecular Systematics. The field of molecular systematics involves the analysis of genetic data, such as DNA sequences or amino acid sequences, to identify and study genetic homologies and propose phylogenetic trees. In 1963, Austrian biologist Emile Zuckerkandl and American chemist Linus Pauling were the first to suggest that molecular data could be used to establish evolutionary relationships. How can a comparison of genetic sequences help to establish evolutionary relationships? As discussed later in this chapter, DNA sequences change over the course of many generations due to the accumulation of mutations. Therefore, when comparing homologous sequences in different species, DNA sequences from closely related species are more similar to each other than they are to sequences from distantly related species. Pg. 155 Likewise, the concept of shared derived characters can apply to molecular data, such as a gene sequence. Let's consider an example to illustrate this idea. Our example involves molecular data obtained from seven different hypothetical plant species called A—G. In these species, a homologous region of DNA was sequenced as shown here: A: GATAGTACCC B: GATAGTTCCC C: GATAGTTCCG D: GGTATTACCC E: GGTATAACCC F: GGTAGTACCA G: GGTAGTACCC The cladogram of figure 26.10 is a hypothesis of how these DNA sequences arose. A mutation that changed the sequence of nucleotides is comparable to a modification of a character. For example, let's designate species D as an outgroup and species A, B, C, F, and G as the ingroup. In this case, a G (guanine) at the fifth position is a shared derived character. The genetic sequence carrying this G is derived from an older primitive sequence. Pg. 157 The principle of parsimony can be applied to the analysis of data on gene sequences. In this case, the most likely hypothesis is the one requiring the fewest base changes. Pg. 158 Cooper and Colleagues Compared DNA from Extinct Flightless Birds and Existing Species to Propose a New Phylogenetic Tree · Genetic sequence information is primarily used for studying relationships among existing species. However, in some cases, DNA can be obtained from extinct organisms. Starting with small tissue samples (usually bone, dried muscle, or preserved skin) from extinct species, scientists have discovered that it is occasionally possible to obtain DNA sequence information. This approach is called ancient DNA analysis, or molecular paleontology. · Since the mid-1980s, some researchers have become excited about the information derived from sequencing DNA of extinct specimens. Debate has centered on how long DNA can remain intact after an organism has died. Over time, the structure of DNA is degraded by hydrolysis and the loss of purines. Nevertheless, under certain conditions (such as cold temperature and low oxygen, and so on), DNA samples may be stable for as long as 50,000-100,000 years. · In recent years, this approach has been used to study evolutionary relationships between living and extinct species. As shown in Figure 26.11, Alan Cooper, Cécile Mourer-Chauviré, Geoffrey Chambers, Arndt von Haeseler, Allan Wilson, and Svante Paabo investigated the evolutionary relationships among some extant and extinct species of flightless birds. In this example of discovery-based science, the researchers gathered data with the goal of proposing a hypothesis about the evolutionary relationships among several bird species. The kiwis and moas are two groups of flightless birds that existed in New Zealand during the Pleistocene. Species of kiwis still exist, but the moas are now extinct. Eleven known species of moas formerly existed. In this study, the researchers investigated the phylogenetic relationships among four extinct species of moas, which were available as museum samples; three species of New Zealand kiwis; and living species of other flightless birds, including the emu and the cassowary (both found in Australia and/or New Guinea), the ostrich (found in Africa and formerly Asia), and two rheas (found in South America). · Samples from the various species were subjected to polymerase chain reaction (PCR) to amplify a region of the gene that encodes SSU rRNA (an RNA found in the small subunits of mitochondrial ribosomes of all organisms, as discussed in Chapter 12). This provided enough DNA for sequencing. The data in Figure 26,11 illustrate a comparison of the sequences of a continuous region of the SSU rRNA gene from these species. The first line shows the DNA sequence for one of the four extinct moa species. Below it are the sequences of several of the other species that were analyzed. When the other sequences are identical to the first sequence, a dot is placed in the corresponding position. When the sequences are different, the changed nucleotide base (A, T, G, or C) is placed there. In a few regions, the genes are different lengths In these cases, a dash I placed to indicate missing nucleotides. · As you can see from the large number of dots, the gene sequences among these flightless birds are very similar, though some differences occur. If you look carefully at the data, you will notice that the sequence of the kiwi (a New Zealand species) is actually more similar to the sequence from the ostrich (an African species) than it is to that of the moa, which was once found in New Zealand. Likewise, the kiwi is more similar to the emu and cassowary (found in Australia and New Guinea) than to the moa. How were these results interpreted? The researchers concluded that the kiwis are more closely related to African and Australian flightless birds than they are to the moas. From these results, they concluded that New Zealand was colonized twice by ancestors of flightless birds. The researchers used a maximum likelihood analysis to propose a new phylogenetic tree that illustrates the revised relationships among these living and extinct species. Pg. 160 26.4 Molecular Clocks · As we have seen, researchers employ different methods to choose a phylogeny that describes the evolutionary relationships among various species. Researchers are interested not only in the most likely pathway of evolution (the branches of the trees), but also the timing of evolutionary change (the lengths of the branches). How can researchers determine when different species diverged from each other in the past? As shown earlier in Figure 26.7, the fossil record can sometimes help researchers apply a timescale to a phylogeny. · Another way to infer the timing of past events is by analyzing genetic sequences. The neutral theory of evolution proposes that most genetic variation that exists in populations is due to the accumulation of neutral mutations—changes in genes and proteins that are not acted on by natural selection. The reasoning behind this concept is that favorable mutations are likely to be very rare and detrimental mutations are likely to be eliminated from a population by natural selection. A large body of evidence supports the idea that much of the genetic variation observed in living species is due to the accumulation of neutral mutations. From an evolutionary point of view, if neutral mutations occur at a relatively constant rate, they can serve as a molecular clock to measure evolutionary time. In this section, we will consider the concept of a molecular clock and its application in phylogenetic trees. Pg. 160 The Timing of Evolutionary Change May Be Inferred from Molecular Clock Data · Figure 26.13 illustrates the concept of a molecular clock. The graph's vertical axis measures the number of base differences in a homologous gene between different pairs of species. The horizontal axis plots the amount of time that has elapsed since each pair of species shared a common ancestor. As shown in the figure, the number of base differences is lower when two species shared a common ancestor in the more recent past than it is for pairs that shared a more distant common ancestor. The explanation for this phenomenon is that the gene sequences of various species accumulate independent mutations after they have diverged from each other. A longer period of time since their divergence allows for a greater accumulation of mutations, which makes their sequences of bases more different. · Figure 26.13 suggests a linear relationships between the number of base changes and the time of divergence. For example, a linear relationship predicts that a pair of species with, say, 20 base differences in a given gene sequence would have a common ancestor that lived roughly twice as long ago as a pair showing 10 nucleotide differences. Although actual data sometimes show a relatively linear relationship over a defined time period, evolutionary biologists do not think that molecular clocks are perfectly linear over very long periods of time. Several factors can contribute to the nonlinearity of molecular clocks. These include difference sin the generation times of the species being analyzed and variation in the mutation rates of genes between different species. · To obtain reliable data, researchers must calibrate their molecular clocks. How much time does it take to accumulate a certain percentage of base changes? To perform such a calibration, researchers must have information regarding the date when two species diverged from a common ancestor. Such information could come from the fossil record, for instance. The genetic differences between those species are then divided by the amount of time since their last common ancestor to calculate a rate of evolutionary change. · As an example of clock calibration, let's consider primates. The fossil evidence suggests that humans and chimpanzees diverged from a common ancestor approximately 6 mya. The percentage of base differences between the mitochondrial DNA of humans and chimpanzees is 12%. From these data, the molecular clock for change sin the sequence of bases in mitochondrial DNA of primates is calibrated at roughly 2% base changes per million years. However, molecular dating based on the use of a single fossil as a calibration point can lead to significant inaccuracies in the molecular clock. When possible, researchers advocate using multiple fossils in the calibration process. Pg. 161 Different Genes Are Analyzed to Study Phylogeny and Evaluate the Timing of Evolutionary Change · For evolutionary comparisons, the DNA sequences of many genes have been obtained from a wide range of sources. Many different genes have been studied to propose phylogenetic trees and evaluate the timeliness of past events. For example, the SSU rRNA gene used by Cooper and colleagues in their research on flightless birds (see Figure 26,11) is commonly used in evolutionary studies. As noted in Chapter 12, the gene for SSU rRNA is found in the genomes of all living organisms. Therefore, its function must have been established at an early stage in the evolution of life on this planet, and its sequence has changed fairly slowly. Furthermore, SSU rRNA is a rather large molecule, so it contains a large amount of sequence information. This gene has been sequenced from thousands of different species (see Figure 12.17). Slowly changing genes such as the gene that encodes SSU rRNA are useful for evaluating distant evolutionary relationships, such as comparing higher taxa. For example, SSU rRNA data can be used to place eukaryotic species into their proper phyla or orders. · Other genes have changed more rapidly during evolution because of a greater tolerance of neutral mutations. For example, the mitochondrial genome and DNA sequences within introns can more easily incur neutral mutations (compared to the coding sequences of genes), and so their sequences change frequently during evolution. More rapidly changing DNA sequences have been used to study recent evolutionary relationships, particularly among eukaryotic species such as species of large animals that have long generation times and therefore tend to evolve more slowly. In these cases, slowly evolving genes may not be very useful for establishing evolutionary relationships because two closely related species may have identical or nearly identical DNA sequences for such genes. · Figure 26.14 shows a simplified phylogeny of closely related species of primates. A molecular clock was used to give a timescale to this phylogenetic tree. The tree was proposed by comparing DNA sequence changes in the gene for cytochrome oxidase subunit II, one of several subunits of cytochrome oxidase, a protein in the mitochondrial inner membrane that is involved in cellular respiration. This gene tends to change fairly rapidly on an evolutionary timescale. The vertical scale on Figure 26.14 represents time, and the branch points labeled with letters represent common ancestors. Let's take a look at the branch points (labeled A, D, and E) and relate them to the accumulation of neutral mutations. o Ancestor A: This ancestor diverged into two species that ultimately gave rise to siamangs and the other five species. Since this divergence, there has been a long time (approximately 23 million years) for the siamang genome to accumulate a relatively high number of random neutral changes that would be different from the random changes that have occurred din the genomes of the other five species (See the yellow bar in Figure 26.14). Therefore, the gene in the siamangs is fairly different form the genes in the other five species. o Ancestor D: This ancestor diverged into two species that eventually gave rise to humans and chimpanzees. This divergence occurred a moderate time ago, approximately 6 mya, as illustrated by the red bar. The differences in gene sequences between humans and chimpanzees are relatively moderate. o Ancestor E: This ancestor diverged into two species of chimpanzees. Since the divergence of species E into two species, approximately 3 mya, the time for the molecular clock to "tick" (that is, accumulate random mutations) is relatively short, as depicted by the green bar in Figure 26.14. Therefore, the two existing species of chimpanzees have fewer differences in their gene sequences compared to other primates. Pg. 162 26.5 Horizontal Gene Transfer · Thus far, we have considered various ways to propose phylogenetic trees, which describe the relationships between ancestors and their descendents. The type of evolution depicted in previous figures, which involves changes in groups of species due to descent from a common ancestor, is sometimes called vertical evolution. Since the time of Darwin, vertical evolution ahs bene the traditional way biologists have viewed the evolutionary process. However, over the past couple of decades, researchers have come to realize that evolution is not so simple. In addition to vertical evolution, horizontal gene transfer has also played a significant role in the phylogeny of living species. · As discussed in Chapters 1 and 23, horizontal gene transfer (also called lateral gene transfer) is used to describe any process in which an organism incorporates genetic material from another organism without being the offspring of that organism. As discussed next, this phenomenon has reshaped the way biologists view the evolution of species. Pg. 162 Genomes & Proteomes Connection Due to Horizontal Gene Transfer, the "Tree of Life" Is Really a "Web of Life" · Horizontal gene transfer has played a major role in the evolution of many species. As discussed in Chapter 18, bacteria can transfer genes via conjugation, transformation, and transduction. Bacterial gene transfer can occur between strains of the same species or, occasionally, between cells of different bacterial species. The transferred genes may encode proteins that provide a survival advantage, such as resistance to antibiotics or the ability to metabolize an organic molecule in the environment. Horizontal gene transfer is also fairly common among certain unicellular eukaryotes. However, its relative frequency and importance in the evolution of multicellular eukaryotic organisms remains difficult to evaluate. · Scientists have debated the role of horizontal gene transfer in the earliest stages of evolution, prior to the divergence of the bacterial and archaeal domains. The traditional viewpoint was that the three domains of life—Bacteria, Archaea, and Eukarya—arose from a single type of prokaryotic (or pre-prokaryotic) cell called the universal ancestor. However, genomic research has suggested that horizontal gene transfer may have been particularly common during the early stages of evolution on Earth, when all species were unicellular. Horizontal gene transfer may have been so prevalent that the universal ancestor may have actually been an ancestral community of cell lineages that evolved as a whole. If that were the case, the three of life cannot be traced back to a single ancestor. · Figure 26.15 illustrates a schematic scenario for the evolution of life that includes the roles of both vertical evolution and horizontal gene transfer. This has been described as a "web of life" rather than a "tree of life." In this scenario, instead of a universal ancestor, a community of primitive cells frequently transferred genetic material in a horizontal fashion. Horizontal gene transfer was also prevalent during the early evolution of bacteria and archaea, and when eukaryotes first emerged as a unicellular species. In living bacteria and archaea, it remains a prominent way to foster evolutionary change. By comparison, the region of the diagram that contains most eukaryotic species has a more treelike structure. Researchers have speculated that multicellularity and sexual reproduction have presented barriers to horizontal gene transfer in most eukaryotes. For a gene to be transmitted to eukaryotic offspring, it would have to be transferred into a eukaryotic cell that is a gamete or a cell that gives rise to gametes. Horizontal gene transfer has become less common in eukaryotes, particularly among multicellular species, though it does occur occasionally.

Differentiate between cladogenesis and anagenesis

New species can be formed by anagenesis, in which a single species evolves into a different species, or much more commonly by cladogenesis, in which a species diverges into two or more species.

Construct a phylogeny using cladistical methods

Now that we have an understanding of shared primitive and derived characters, let's consider the steps a researcher would follow to propose a cladogram using a cladistics approach. 1) Choose the species whose evolutionary relationships are of interest. In a simple cladogram, such as those described in this chapter, individual species are compared with each other. In more complex cladograms, species may be grouped into larger taxa (for example, families) and compared with each other. If such grouping is done, the results are not reliable if the groups are not clades. 2) Choose characters for comparing the species selected in step 1. As mentioned, a character is a general feature of an organism and may come in different versions called character states. For example, a front limb is a character in mammals, which could exist in different character states such as a wing, an arm, or a flipper. 3) Determine the polarity of character states. In other words, determine if a character state came first and is primitive or came later and is a derived character. This information may be available by examining the fossil record, for example, but is usually done by comparing the ingroup with the outgroup. For a character with two character states, an assumption is made that a character state shared by the outgroup and ingroup is primitive. A character state shared only by members of the ingroup is derived. 4) Analyze cladograms based on the following principles: a. All species (or higher taxa) are placed on tips in a phylogenetic tree, not at branch points b. Each cladogram branch point should have a list of one or more shared derived characters that are common to all species above the branch point unless the character is later modified c. All shared derived characters appear together only once in a cladogram unless they arose independently during evolution more than once. 5) Among many possible options, choose the cladogram that provides the simplest explanation for the data. A common approach is to use a computer program that generates many possible cladograms. Analyzing the data and choosing among the possibilities are key aspects of this process. As described later, different theoretical approaches, such as the principle of parsimony, can be used to choose among possible phylogenies. 6) Provide a root to the phylogenetic tree by choosing a noncontroversial outgroup. In this textbook, most phylogenetic trees are rooted, which means that a single node at the bottom of the tree corresponds to a common ancestor for all of the species or groups of species in the tree. A method for rooting trees is the use of a noncontroversial outgroup. Such an outgroup typically shares morphological traits and/or DNA sequence similarities with the members of the ingroup, to allow a comparison between the ingroup and outgroup. Even so, the outgroup must be non-controversial in that it has enough distinctive differences with the ingroup to be considered a clear outgroup. For example, if the ingroup was a group of mammalian species, an outgroup could be a reptile.

Differentiate between taxonomy, a phylogeny, and systematics.

Taxonomy (pg 147)- Taxonomy is the science of describing, naming, and classifying extant species, those that still exist today, as well as extinct species, those that have died out. Taxonomy results in the ordered division of species into groups based on similarities and dissimilarities in their characteristics. This task has been ongoing for over 300 years. As discussed in Chapter 23, the naturalist John Ray made the first attempt to broadly classify all known forms of life. Ray's ideas were later extended by naturalist Carolus Linnaeus in the mid-1700s, which is considered by some as the official birth of taxonomy. Systematics (pg 147)- Is the study of biological diversity and the evolutionary relationships among species, both extant and extinct. In the 1950s, German entomologist Willi Hennig began classifying species in a new way. Hennig proposed that evolutionary relationships should be inferred from features shared by descendants of a common ancestor. Since that time, biologists have applied systematics to the field of taxonomy. Researchers now try to place new species into taxonomic groups based on evolutionary relationships with other species. In addition, previously established taxonomic groups are revised as new data shed light on evolutionary relationships. Like any other scientific discipline, taxonomy should be viewed as a work in progress. · A phylogeny (pg 150)- Biologists use systematics to determine evolutionary relationships among species, looking in particular at how these relationships are portrayed in diagrams called phylogenetic trees. o By studying the similarities and differences among species, biologists can construct a phylogeny, which is the evolutionary history of a species or group of species. To propose a phylogeny, biologists use the tools of systematics. For example, the classification of the gray wolf in Figure 26.2 is based on systematics. Therefore, one use of systematics is to place species into taxa and to understand the evolutionary relationships among different taxa. o Phylogenetic tree- a phylogenetic tree is a diagram that describes the evolutionary relationships among various species, based on the information available to and gathered by systematists. Phylogenetic trees should be viewed as hypotheses that are proposed, tested, and later refined as additional data becomes available.

Describe the Principle of Parsimony and its application to cladistics

The Principle of Parsimony Is Used to Choose from Among Possible Cladograms One approach for choosing among possible cladograms is to assume that the best hypothesis is the one that requires the fewest number of evolutionary changes. This concept, called the principle of parsimony, states that the preferred hypothesis is the one that is the simplest for all the characters and their states. For example, if two species possess a tail, we would initially assume that a tail arose once during evolution and that both species have descended from a common ancestor with a tail. Such a hypothesis is simpler, and more likely to be correct, than assuming that tails arose twice during evolution and that the tails in the two species are not due to descent from a common ancestor.

Differentiate between symplesiomorphies and synapomorphies and determine which one is more useful in cladistics (pg 154).

To understand the cladistics approach, let's take a look at a simplified phylogeny (figure 26.8). We can place the species that currently exist into two groups: D and E, and F and G. The most recent common ancestor to D and E is B, whereas species C is the most recent common ancestor to F and G. With these ideas in mind, let's focus on the front limbs (flippers versus legs) and eyes. A character trait that is shared by two or more different taxa and inherited from ancestors older than their last common ancestor is called a shared primitive character, or symplesiomorphy. Such characters are viewed as being older—ones that occurred earlier in evolution. With regard to species D, E, F, and G, having two eyes is a shared primitive character. It originated prior to species B and C. By comparison, a shared derived character, or synapomorphy, is a character that is shared by two or more species or taxa and has originated in their most recent common ancestor. With regard to species D and E, having two front flippers is a shared derived character that originated in species B, their most recent common ancestor (see figure 26.8). Compared with shared primitive characters, shared derived characters are more recent traits on an evolutionary timescale. For example, among mammals, only some species, such as whales and dolphins, have flippers. In this case, flippers were derived from the two front limbs of an ancestral species. The word derived indicates that evolution involves the modification of traits in pre-existing species. In other words, populations of organisms with new traits are derived from changes in pre-existing populations. The basics of the cladistic approach is to analyze many shared derived characters among groups of species to deduce the pathway that gave rise to those species. Note that the terms primitive and derived do not indicate the complexity of a character. For example, the flippers of a dolphin do not appear more complex than the front limbs of ancestral species A, which were limbs with individual toes. Derived characters can be similar in complexity, less complex, or more complex than primitive characters. · Shared derived characters, or synapomorphies, are more useful in cladistics. Since current evolutionary theory says that traits arise (are derived) in lineages through evolution, only synapomorphies can be used to establish relationships. Symplesiomorphies should not be used to unite taxa.

Differentiate between a monophyletic group, a paraphyletic group, and a polyphyletic group.

· A monophyletic group (pg 150)- A key goal of modern systematics is to create taxonomic groups that reflect evolutionary relationships. Systematics attempts to organize species into clades, which means that each group includes an ancestral species and all of its descendants. ****A monophyletic group is a taxon that is a clade. Ideally, every taxon, whether it is a domain, supergroup, kingdom, phylum, class, order, family, or genus, should be a monophyletic group. What is the relationship between a phylogenetic tree and taxonomy? The relationship depends on how far back we go to identify a common ancestor. For broader taxa, such as a kingdom, the common ancestor existed a very long time ago, on the order of hundreds of millions or even billions of years ago. For smaller taxa, such as a family or genus, the common ancestor occurred much more recently, on the order of millions or tens of millions of years ago. This concept is shown in a schematic way in Figure 26.4. This small, hypothetical kingdom is a clade that contains 64 living species. (Actual kingdoms are obviously larger and exceedingly more complex.) The diagram emphasizes the taxa that contain the species designated number 43. The common ancestor that gave rise to this kingdom existed approximately 1 billion years ago. Over time, more recent species arose that subsequently became the common ancestors to the phylum, class, order, family, and genus that contain species number 43. · How does research in systematics affect taxonomy? As researchers gather new information, they sometimes discover that some of the current taxonomic groups are not monophyletic. Figure 26.5 compares a monophyletic group with taxonomic groups that are not. ****A paraphyletic group contains a common ancestor and some, but not all, of its descendants. · ****In contrast, a polyphyletic group consists of members of several evolutionary lines and does not include the most recent common ancestor of the included lineages. · As scientists learn more about evolutionary relationships, taxonomic groups are reorganized to recognize only monophyletic groups. For example, traditional classification schemes once separated birds and reptiles into separate classes (Figure 26.6a). In this scheme, the reptile class (officially named Reptilia) contained orders that included turtles, lizards and snakes, and crocodiles, with birds constituting a different class. Research indicated that the reptile taxon was paraphyletic, because birds were excluded from the group. This group can be made monophyletic by including birds as a class within the reptile clade and elevating the other groups to a class status.

Identify what types of organisms are found in each of the three domains of life

· All forms of life are grouped within three domains: Bacteria, Archaea, and Eukarya. o The terms Bacteria and Archaea are capitalized when referring to the domains, but are not capitalized when referring to individual species. A single bacterial cell is called a bacterium, and a single archaeal cell is an archaeon. Modern taxonomy places species into progressively smaller hierarchial groups. Each group at any level is called a taxon (plural, taxa). The taxon called the kingdom was originally the highest and most inclusive. Linnaeus had classified all life into two kingdoms, plants and animals. In 1969, American ecologist Robert Whittaker proposed a five-kingdom system in which all life was classified into the kingdoms Monera, Protista, Fungi, Plantae, and Animalia. However, as biologists began to learn more about the evolutionary relationships among these groups, they found that this classification did not correctly reflect the relationships among them. In the late 1970s, based on information in the sequences of genes, American biologist Carl Woese proposed the idea of creating a category called a domain. In the taxonomy hierarchy, a domain is above a kingdom. Under this system, all forms of life are grouped within three domains: Bacteria, Archaea, and Eukarya. The terms Bacteria and Archaea are capitalized when referring to the domains, but are not capitalized when referring to individual species. A single bacterial cell is called a bacterium, and a single archaeal cell is called an archaeon. The domain Eukarya formerly consisted of four kingdoms called Protista, Fungi, Plantae, and Animalia. However, researchers later discovered that protists do not constitute a separate kingdom but instead are a very broad collection of species. Taxonomists now place most eukaryotes into seven groups called supergroups. In the taxonomy of eukaryotes, a supergroup lies between a domain and a kingdom. As discussed in Chapter 28, all seven supergroups contain a distinctive group of protists. In addition, kingdoms Fungi and Animalia are within the supergroup Opisthokonta, because they are closely related to the protists in this supergroup. Kingdom Plantae is within the supergroup called Land plants and relatives. Plants are closely related to green algae, which are protists in this supergroup. Table 26.1 compares a variety of molecular and cellular characteristics among the domains Bacteria, Archaea, and Eukarya. · Bacteria- Prokaryotes (does not have distinct nucleus to enclose it). Unicellular. Don't have membrane bound organelles. Chemotroph, get their energy from chemicals. Binary fission to reproduce. · Archaea- Prokaryotes (does not have distinct nucleus to enclose it). Unicellular. More closely related to eukaryotes. Don't have membrane bound organelles. RNA polymerase much more like eukarya. Chemotroph, get their energy from chemicals. Can live in extreme environments, like extreme temperatures and high salt levels. Binary fission to reproduce. · Eukarya- Make up all of the life forms with a nucleus. Consist of kingdoms Protista, fungi, plantae, and animalia. These four categories are a human creation. We looked at life and divided it up based on what we saw. o Protists- Single celled organisms. Contains both autotrophs and heterotrophs. Some protists can photosynthesize while others eat living things. Protists are a bunch of weird eukaryotic single-celled organisms (usually single-celled) that may or may not be evolutionarily related to each other. Some are plant-like, like algae. Some are more animal-like, like amoebas. Some are fungus like, like slime mold. Protists is a gray area. o Fungi- Heterotrophs, meaning they get their energy from eating other organisms. Include mushrooms, smuts, puffballs, truffles, molds, yeast. They have cell walls like plants but instead of being made of cellulose they are made of another carbohydrate called chitin. Since they are heterotrophs like animals, they have digestive enzymes that break down their food and get reabsorbed but they can't move, so they don't require a stomach for digestion. They just grow on top of whatever they're digesting and digest right where it is. o Plantae- Autotrophs, means they can feed themselves through photosynthesis. Cellulose based cell walls and chloroplasts giving them a distinct difference from al other multicellular life. o Animalia- Heterotrophs, meaning they get their energy from eating other organisms. Always multicellular. Almost all of us can move at least during some stage of our life cycle. Most of us develop either two or three germ layers during embryonic development unless you're a sponge. Prokaryotes lack a nucleus and are single-celled organisms and lack membrane-bound organelles