POB Ch 21
One that is highly subject to environmental modification Which morphological trait would a biologist most likely exclude from use in phylogenetic analysis?
Giraffes are in the genus Giraffa. Their family is named after this genus. Hence, the family name is written Correct: Giraffidae.
Some species of Drosophila have elaborate "picture wings," whereas most others do not. Which type of evidence would most likely suggest that the elaborate picture wings evolved via convergent evolution? Correct: Picture wings are found in different clades of flies.
Which taxonomic category is next smallest than a phylum? Class
phylogenetic tree: A graphic representation of the evolutionary history of a particular group of organisms or their genes.
phylogeny: (fy loj′ e nee) [Gk. phylon: tribe, race + genesis: source] The evolutionary history of a particular group of organisms or their genes. A phylogenetic tree is a graphic representation of these lines of evolutionary descent.
Male swordtails—a group of fish in the genus Xiphophorus—have a long, colorful tail extension, and their reproductive success is closely associated with this appendage. Males with a long sword are more likely to mate successfully than are males with a short sword (an example of sexual selection; see Key Concept 20.2). Several explanations have been advanced for the evolution of this structure, including the hypothesis that the sword simply exploits a preexisting bias in the sensory system of the females. This sensory exploitation hypothesis suggests that female swordtails had a preference for males with long tails even before the tails evolved (perhaps because females assess the size of males by their total body length—including the tail—and prefer larger males). To test the sensory exploitation hypothesis, phylogenetic analysis was used to identify the relatives of swordtails that had split most recently from their lineage before the evolution of swords. These closest relatives turned out to be fish in the genus Priapella. Even though male Priapella do not normally have swords, when researchers attached artificial swordlike structures to the tails of male Priapella, female Priapella preferred those males. This result provided support for the hypothesis that female Xiphophorus had a preexisting sensory bias favoring tail extensions even before the trait evolved (Figure 21.9). Thus a long tail became a sexually selected trait because of the preexisting preference of the females. The phylogeny allows us to understand when the trait evolved relative to the change in female preference.
HIV-1 is the common form of the virus in human populations in central Africa, where chimpanzees are hunted for food, and HIV-2 is the common form in human populations in western Africa, where sooty mangabeys are hunted for food. Thus it seems likely that these viruses entered human populations through hunters who cut themselves while skinning chimpanzees and sooty mangabeys. The global pandemic of AIDS occurred when these infections in local African populations rapidly spread through human populations around the world. In recent years, phylogenetic analysis has become important in forensic investigations that involve viral transmission events. For example, phylogenetic analysis was critical for a criminal investigation of a physician who was accused of purposefully injecting blood from one of his HIV-positive patients into his former girlfriend in an attempt to kill her. The phylogenetic analysis revealed that the HIV strains present in the girlfriend were a subset of those present in the physician's patient (Figure 21.8). Other evidence was needed, of course, to connect the physician to this purposeful transmission event, but the phylogenetic analysis was important to support the viral transmission event from the patient to the victim.
Because of the historical separation of the fields of zoology, botany (which originally included mycology, the study of fungi), and microbiology, different sets of taxonomic rules were developed for each of these groups. Yet another set of rules emerged later for classifying viruses. This separation of fields resulted in duplicated taxon names in groups governed by the different sets of rules. Drosophila, for example, is both a genus of fruit flies and a genus of fungi, and some species in both groups have identical names. Until recently these duplicated names caused little confusion, since traditionally biologists who studied fruit flies were unlikely to read the literature on fungi (and vice versa). Today, given the prevalence of large, universal biological databases (such as GenBank, which includes DNA sequences from across all life), it is increasingly important that each taxon have a unique and unambiguous name. Biologists are working on a universal code of nomenclature that can be applied to all organisms, so that every species will have a unique identifying name or registration number. This will assist efforts to build an online Encyclopedia of Life that links all the information for all the world's species.
Several sets of explicit rules govern the use of scientific names. Biologists around the world follow these rules voluntarily to facilitate communication and dialogue. There may be dozens of common names for an organism in many different languages, and the same common name may refer to more than one species (Figure 21.14). The rules of biological nomenclature are designed so that there is only one correct scientific name for any single recognized taxon, and (ideally) a given scientific name applies only to a single taxon (that is, each scientific name is unique). Sometimes the same species is named more than once (when more than one taxonomist has taken up the task). In these cases, the rules specify that the valid name is the first name that was proposed. If the same name is inadvertently given to two different species, then the species that was named second must be given a new name.
All synapomorphies are shared traits. Which statement about traits and phylogeny is true?
Suppose a biologist has data showing both the divergence times between species and the number of changes at a gene for the species. Now suppose that the biologist plots divergence time on the x axis and the number of changes on the y axis. If a molecular clock is operating, then the slope of that curve must be Constant
The biological classification system in widespread use today is derived from a system developed by the Swedish biologist Carolus Linnaeus in the mid-1700s. Linnaeus developed a naming system called binomial nomenclature that has allowed scientists throughout the world to refer unambiguously to the same organisms by the same names.
Phylogenetic trees are used to reconstruct the evolutionary history of lineages, to determine when and where traits arose, and to make biological comparisons among genes, populations, and species. They can also be used to reconstruct ancestral traits and to estimate the timing of evolutionary events.
Lineages of mammals with short generation times evolve faster than lineages with longer generation times. Which scenario presents the greatest challenge to the assumption of a molecular clock?
All human viruses would form a single clade. Which would be the signature that a human virus was acquired from a single animal source?
Molecular clocks help date evolutionary events... For many applications, biologists want to know not only the order in which evolutionary lineages split but also the timing of those splits. In 1965, Emile Zuckerkandl and Linus Pauling hypothesized that rates of molecular change were constant enough that they could be used to predict evolutionary divergence times—an idea that has become known as the molecular clock hypothesis. Of course, different genes evolve at different rates, and there are also differences in evolutionary rates among species related to differing generation times, environments, efficiencies of DNA repair systems, and other biological factors. Nonetheless, among closely related species, a given gene usually evolves at a reasonably constant rate. Therefore the protein encoded by the gene accumulates amino acid replacements at a relatively constant rate (Figure 21.11). A molecular clock uses the average rate at which a given gene or protein accumulates changes to gauge the time of divergence for a particular split in the phylogeny. Molecular clocks must be calibrated using independent data, such as the fossil record, known times of divergence, or biogeographic dates (e.g., the time of separations of continents). Using such calibrations, times of divergence have been estimated for many groups of species that have diverged over millions of years. Molecular clocks are not only used to date ancient events; they are also used to study the timing of comparatively recent events. Most samples of HIV-1 have been collected from humans only since the early 1980s, although a few isolates from medical biopsies are available from as early as the 1950s. Biologists can use the observed changes in HIV-1 over the past several decades to project back to the common ancestor of all HIV-1 isolates, and estimate when HIV-1 first entered human populations from chimpanzees (Figure 21.12). This molecular clock was calibrated using the samples from the 1980s and 1990s, and then tested using the samples from the 1950s. As shown in Figure 21.12C, a sample from a 1959 biopsy is dated by molecular clock analysis at 1957 ± 10 years. Extrapolation back to the common ancestor of the samples suggested a date of origin for this group of viruses of about 1930. Although AIDS was unknown to Western medicine until the 1980s, this analysis shows that HIV-1 was present (probably at a very low frequency) in human populations in Africa for at least a half-century before its emergence as a global pandemic. Biologists have used similar analyses to conclude that immunodeficiency viruses have been transmitted repeatedly into human populations from multiple primates for more than a century (see also Figure 21.7).
Ancestral states can be reconstructed In addition to using phylogenetic methods to infer evolutionary relationships, biologists can use these techniques to reconstruct the morphology, behavior, or nucleotide and amino acid sequences of ancestral species (as was demonstrated for the ancestral sequence of bacteriophage T7 in Investigating Life: Testing the Accuracy of Phylogenetic Analysis). In the opening of this chapter, we described how Mikhail Matz used phylogenetic analysis to reconstruct the sequence of changes in fluorescent proteins of corals to understand how red fluorescent proteins could be produced. Reconstruction of ancient DNA sequences can also provide information about the biology of long-extinct organisms. For example, phylogenetic analysis was used to reconstruct an opsin protein in the ancestral archosaur (the most recent common ancestor of birds, dinosaurs, and crocodiles). Opsins are pigment proteins involved in vision; different opsins (with different amino acid sequences) are excited by different wavelengths of light. Knowledge of the opsin sequence in the ancestral archosaur would provide clues about the animal's visual capabilities and therefore about some of its probable behaviors. Investigators used phylogenetic analysis of opsin from living vertebrates to estimate the amino acid sequence of the pigment that existed in the ancestral archosaur. A protein with this same sequence was then constructed in the laboratory. The investigators tested the reconstructed opsin and found a significant shift toward the red end of the spectrum in the light sensitivity of this protein compared with that of most modern opsins. Modern species that exhibit similar sensitivity are adapted for nocturnal vision, so the investigators inferred that the ancestral archosaur might have been active at night. Thus, reminiscent of the movies Jurassic Park and Jurassic World, phylogenetic analyses are being used to reconstruct extinct species, one protein at a time.
Before the 1980s, phylogenetic trees tended to be seen only in the literature on evolutionary biology, especially in the area of systematics—the study and classification of biodiversity. But almost every journal in the life sciences published during the last few years contains phylogenetic trees. Trees are widely used in molecular biology, biomedicine, physiology, behavior, ecology, and virtually all other fields of biology. Why have phylogenetic studies become so widespread? Likewise, biologists use phylogenies to make comparisons and predictions about shared traits across genes, populations, and species.
Any group of species that we designate with a name is a taxon (plural taxa). Examples of familiar taxa include humans, primates, mammals, and vertebrates; in this series, each taxon is also a member of the next, more inclusive taxon. Any taxon that consists of all the evolutionary descendants of a common ancestor is called a clade. Clades can be identified by picking any point on a phylogenetic tree and from that point tracing all the descendant lineages to the tips of the terminal branches (Figure 21.3). Two species that are each other's closest relatives are called sister species. Similarly, any two clades that are each other's closest relatives are sister clades.
The reconstructed phylogeny suggests that self-incompatibility is the ancestral state and that self-compatibility evolved three times within this group of Leptosiphon. The change to self-compatibility eliminated the plants' dependence on an outside pollinator and has been accompanied by the evolution of reduced petal size. Indeed, the striking morphological similarity of the flowers in the self-compatible groups once led to their being classified as members of a single species (L. bicolor). Phylogenetic analysis, however, shows them to be members of three distinct lineages. From this information we can infer that self-compatibility and its associated floral structure are convergent in the three independent lineages that had been called L. bicolor. Phylogenies can reveal convergent evolution!!!!!!
The evolution of angiosperm fertilization mechanisms was examined in Leptosiphon, a genus in the phlox family that exhibits a diversity of mating systems and pollination mechanisms. The self-incompatible (outcrossing) species of Leptosiphon have long petals and are pollinated by long-tongued flies. In contrast, self-pollinating species have short petals and do not require insect pollinators to reproduce successfully. Using ribosomal DNA sequences, investigators reconstructed a phylogeny of this genus (Figure 21.10). They then determined whether each species was self-compatible by artificially pollinating flowers with the plant's own pollen or with pollen from other individuals and observing whether viable seeds formed.
Any features shared by two or more species that have been inherited from a common ancestor are said to be homologous. Homologous features may be any heritable traits, including DNA sequences, protein structures, anatomical structures, and even some behavior patterns. For example, all living vertebrates have a vertebral column, as did the ancestral vertebrate. Therefore the vertebral column is judged to be homologous in all vertebrates.
The evolutionary relationships among species, as represented in the tree of life, form the basis for biological classification. Biologists estimate that there are tens of millions of species on Earth. So far, however, only about 1.8 million species have been classified—that is, formally described and named. New species are being discovered all the time and phylogenetic analyses are constantly reviewed and revised, so our knowledge of the tree of life is far from complete. Yet knowledge of evolutionary relationships is essential for making comparisons in biology, so biologists build phylogenies for groups of interest as the need arises. The tree of life's evolutionary framework allows us to make many predictions about the behavior, ecology, physiology, genetics, and morphology of species that have not yet been studied in detail. When biologists compare species, they observe traits that differ within the group of interest and try to understand when these traits evolved. In many cases, investigators are interested in how the evolution of a trait relates to environmental conditions or selective pressures. For instance, scientists have used phylogenetic analyses to discover changes in the genome of human immunodeficiency viruses (HIVs) that result in resistance to particular drug treatments. The association of a particular genetic change in HIV with a particular treatment provides a hypothesis about the evolution of resistance that can be tested experimentally.
evolutionary reversal: The reappearance of an ancestral trait in a group that had previously acquired a derived trait.
convergent evolution: Independent evolution of similar features from different ancestral traits.
Similar traits generated by convergent evolution and evolutionary reversals are called homoplastic traits or homoplasies. synapomorphy: A trait that arose in the ancestor of a phylogenetic group and is present (sometimes in modified form) in all of its members, thus helping to delimit and identify that group. Also called a shared derived trait.
homoplasy: (home´ uh play zee) [Gk. homos: same + plastikos: shape, mold] The presence in multiple groups of a trait that is not inherited from the common ancestor of those groups. Can result from convergent evolution, evolutionary reversal, or parallel evolution.
If phylogenetic trees represent reconstructions of past events, and if many of these events occurred before any humans were around to witness them, how can we test the accuracy of phylogenetic methods? Biologists have conducted experiments both in living organisms and with computer simulations that have demonstrated the effectiveness and accuracy of phylogenetic methods. In one experiment designed to test the accuracy of phylogenetic analysis, a single viral culture of bacteriophage T7 was used as a starting point, and lineages were allowed to evolve from this ancestral virus in the laboratory (Investigating Life: Testing the Accuracy of Phylogenetic Analysis). The initial culture was split into two separate lineages, one of which became the ingroup for analysis and the other of which became the outgroup for rooting the tree. The lineages in the ingroup were split in two after every 400 generations, and samples of the virus were saved for analysis at each branching point. The lineages were allowed to evolve until there were eight lineages in the ingroup. Mutagens were added to the viral cultures to increase the mutation rate so that the amount of change and the degree of homoplasy would be typical of the organisms analyzed in average phylogenetic analyses. The investigators then sequenced samples from the end points of the eight ingroups and one outgroup lineages, as well as from the ancestors at the branching points. They then gave the sequences from the end points of the lineages to other investigators to analyze, without revealing the known history of the lineages or the sequences of the ancestral viruses. After the phylogenetic analysis was completed, the investigators asked two questions. Did phylogenetic methods reconstruct the known history correctly? And were the sequences of the ancestral viruses reconstructed accurately? The answer in both cases was yes. The branching order of the lineages was reconstructed exactly as it had occurred, more than 98 percent of the nucleotide positions of the ancestral viruses were reconstructed correctly, and 100 percent of the amino acid changes in the viral proteins were reconstructed correctly.
maximum likelihood: A statistical method of determining which of two or more hypotheses (such as phylogenetic trees) best fit the observed data, given an explicit model of how the data were generated. The experiment shown in Investigating Life: Testing the Accuracy of Phylogenetic Analysis demonstrated that phylogenetic analysis was accurate under the conditions tested, but it did not examine all possible conditions. Other experimental studies have taken other factors into account, such as the sensitivity of phylogenetic analysis to convergent environments and highly variable rates of evolutionary change. In addition, computer simulations based on evolutionary models have been used extensively to study the effectiveness of phylogenetic analysis. These studies have also confirmed the accuracy of phylogenetic methods and have been used to refine those methods and extend them to new applications.
MORPHOLOGY An important source of phylogenetic information is morphology: the presence, size, shape, and other attributes of body parts. Since living organisms have been observed, depicted, collected, and studied for millennia, we have a wealth of recorded morphological data as well as extensive museum and herbarium collections of organisms whose traits can be measured. New technological tools, such as the electron microscope and computed tomography (CT) scans, enable systematists to examine and analyze the structures of organisms at much finer scales than was formerly possible. Most species are described and known primarily by their morphology, and morphology still provides the most comprehensive data set available for many taxa. The morphological features that are important for phylogenetic analysis are often specific to a particular group. For example, the presence, development, shape, and size of various features of the skeletal system are important in vertebrate phylogeny, whereas floral structures are important for studying the relationships among flowering plants.
Any trait that is genetically determined, and therefore heritable, can be used in a phylogenetic analysis. Evolutionary relationships can be revealed through studies of morphology, development, the fossil record, behavioral traits, and molecular traits such as DNA and protein sequences. Let's take a closer look at the types of data used in modern phylogenetic analyses. Morphological approaches to phylogenetic analysis have some limitations, however. Some taxa exhibit little morphological diversity, despite great species diversity. Furthermore, some morphological variation has an environmental (rather than a genetic) basis and so must be excluded from phylogenetic analyses. An accurate phylogenetic analysis often requires information beyond that supplied by morphology.
Males with longer swords have increased mating success because females prefer them over other males. Which statement about swordtails or related fish is true?
Biologists have described well over a million species of eukaryotes. Most species that have been described are known primarily by their? Morphology
PALEONTOLOGY The fossil record is another important source of information on evolutionary history. Fossils show us where and when organisms lived in the past and give us an idea of what they looked like. Fossils provide important evidence that helps us distinguish ancestral from derived traits. The fossil record can also reveal when lineages diverged and began their independent evolutionary histories. Furthermore, in groups with few species that have survived to the present, information on extinct species is often critical to an understanding of the large divergences among the surviving species. The fossil record has limitations, however. Few or no fossils have been found for some groups, and the fossil record for many groups is fragmentary. BEHAVIOR Some behavioral traits are culturally transmitted and others are genetically inherited. If a particular behavior is culturally transmitted, it may not accurately reflect evolutionary relationships (but may nonetheless reflect cultural connections).
DEVELOPMENT Similarities in *developmental patterns may reveal evolutionary relationships. Some organisms exhibit similarities only in early developmental stages. The larvae of marine creatures called sea squirts, for example, have a flexible gelatinous rod in the back—the notochord—that disappears as the larvae develop into adults. All vertebrate animals also have a notochord at some time during their development (Figure 21.6). This shared structure is one of the reasons for inferring that sea squirts are more closely related to vertebrates than would be suspected if only adult sea squirts were examined. Development Reveals the Evolutionary Relationship between Sea Squirts and Vertebrates All chordates—a taxonomic group that includes sea squirts and frogs—have a notochord at some stage of their development. The larvae share similarities that are not apparent in the adults. Such similarities in development can provide useful evidence of evolutionary relationships. The notochord is lost in adult sea squirts. In adult frogs, as in all vertebrates, the vertebral column replaces the notochord as the support structure. *connect the concepts Evolutionary developmental biology, the subject of Chapter 19, compares the developmental processes of different organisms to determine the ancestral relationship between them, and to discover how developmental processes evolved. Genetic toolkit genes are expressed in different ways in different species, resulting in major morphological differences among species (see Key Concepts 19.4 and 19.5). The existence of highly conserved development genes makes it likely that similar traits will evolve repeatedly.
parsimony principle: Preferring the simplest among a set of plausible explanations of any phenomenon.
How do we determine which traits are synapomorphies and which are homoplasies? One way is to invoke the principle of parsimony. In its most general form, the parsimony principle states that the preferred explanation of observed data is the simplest explanation. Applying the principle of parsimony to the reconstruction of phylogenies entails minimizing the number of evolutionary changes that need to be assumed over all characters in all groups in the tree. In other words, the best hypothesis under the parsimony principle is one that requires the fewest homoplasies. This application of parsimony is a specific case of a general principle of reasoning called Occam's razor: the best explanation is the one that best fits the data while making the fewest assumptions. More complicated explanations are accepted only when the evidence requires them. Phylogenetic trees represent our best estimates about evolutionary relationships, given our current knowledge. They are continually modified as additional evidence becomes available.
We begin by noting that the chimpanzee and mouse share two traits—mammary glands and fur—that are absent in both the outgroup and in the other species of the ingroup. Therefore we infer that mammary glands and fur are derived traits that evolved in a common ancestor of chimpanzees and mice after that lineage separated from the lineages leading to the other vertebrates. These characters are synapomorphies that unite chimpanzees and mice (as well as all other mammals, although we have not included other mammalian species in this example). By the same reasoning, we can infer that the other shared derived traits are synapomorphies for the various groups in which they are expressed. For instance, keratinous scales are a synapomorphy of the lizard, crocodile, and pigeon.
In a phylogenetic study, the group of organisms of primary interest is called the ingroup. As a point of reference, an ingroup is compared with an outgroup: a species or group that is closely related to the ingroup but is known to be phylogenetically outside it. In other words, the root of the tree is located between the ingroup and the outgroup. Any trait that is present in both the ingroup and the outgroup must have evolved before the origin of the ingroup and thus must be ancestral for the ingroup. In contrast, traits that are present in only some members of the ingroup must be derived traits within that ingroup. As we will see in Chapter 32, a group of jawless fish called the lampreys is thought to have separated from the lineage leading to the other vertebrates before the jaw arose. Therefore we have included the lamprey as the outgroup for our analysis. Because derived traits are traits acquired by other members of the vertebrate lineage after they diverged from the outgroup, any trait that is present in both the lamprey and the other vertebrates is judged to be ancestral.
If phylogenetic trees represent reconstructions of past events without human witnesses, how can we test the accuracy of phylogenetic methods? Biologists have conducted experiments both in living organisms and with computer simulations that have demonstrated the accuracy of phylogenetic methods. One such experiment employed a bacterial virus called bacteriophage T7. A single culture of the virus was used as a starting point, and lineages were allowed to evolve from this ancestral virus in the laboratory. On the culture dish, each round plaque represents a clone of genetically identical viruses. The initial culture was split into two separate lineages, one of which became the ingroup for analysis, and the other became the outgroup for rooting the tree. The test tubes for growing the viruses contained bacteria in a culture broth that was laced with a DNA mutagen. The mutagen increased the frequency of DNA sequence changes from one generation of viruses to the next. A T7 bacteriophage injects its DNA into a host cell of E. coli, resulting in the production of numerous progeny viruses and the lysis of the cell. In this experiment, approximately two generations were allowed to reproduce in a test tube. Let's look at the ingroup. A small sample of viruses was used to inoculate successive fresh cultures of E. coli. After five such cultures, the last generation of viruses was incubated on Petri plates with E. coli. The resulting plaques are clearings in the lawn of bacteria, with each consisting of a pool of identical viruses. A single plaque was picked to start a new culture. This procedure was repeated about 40 times, meaning that the viruses reproduced through roughly 400 generations, all while being exposed to a DNA mutagen. A single plaque from the final generation was then used to inoculate two new series of tubes. We can simplify this flow chart and represent it with a phylogenetic tree. Each node signifies a point at which the lineages were split in two. The outgroup was not split into separate lineages. The lineages of the ingroup were split after every 400 generations, and samples of the virus were saved for analysis at each branching point. The lineages were allowed to evolve until there were eight lineages in the ingroup and one in the outgroup. The investigators then sequenced DNA from viruses at the endpoints of the eight lineages, as well as from the ancestors at the branching points. They gave the sequences from the endpoints to other investigators to analyze, without revealing the known history of the lineages or the sequences of the ancestral viruses. Using the sequence information from the endpoints, the second group of investigators reconstructed the branching order of the lineages exactly as it had occurred. Additionally, the investigators reconstructed with 98% accuracy the nucleotide sequences of the ancestral viruses. This investigation clearly illustrates the validity of phylogenetic reconstruction methods.
In recent years, DNA sequences have become one of the most widely used sources for constructing phylogenetic trees. How can we test the accuracy of these construction efforts, considering that evolutionary events occurred in the past, mostly without human witnesses? Phylogenetic trees represent hypotheses of evolutionary relationships that can be explicitly tested using data. The example described in this animation does just that. A group of investigators set up an experiment to track the evolution of a bacterial virus, called bacteriophage T7, in the laboratory. With the history of the T7 lineages known, the investigators could determine if a phylogenetic construction (based on the DNA sequences of the viruses at the endpoints of the lineages) matched the known history of the lineages. In an experiment to test the accuracy of phylogenetic reconstruction methods, investigators followed the evolution of a bacterial virus as it reproduced over more than 1000 generations. The growth medium during these generations included a mutagen, which caused more nucleotide changes per replication cycle than normal, essentially speeding up evolutionary change. From this experiment, the investigators produced a known phylogenetic tree of 9 lineages. DNA sequences from the viruses at the endpoints of the lineages were given to another set of investigators, who used the sequence to reproduce an accurate phylogenetic tree of the viral lineages. Thus, this experiment provided a known phylogenetic tree that allowed the investigators to declare that their phylogenetic reconstruction was indeed accurate.
Superficially similar traits may evolve independently in different lineages, a phenomenon called convergent evolution. For example, although the wing bones of bats and birds are homologous, having been inherited from a common tetrapod ancestor, the wings of bats and birds are not homologous because they evolved independently from the forelimbs of different nonflying ancestors (Figure 21.4). Functionally similar structures that have independent evolutionary origins are called analogous characters. A character may revert from a derived state back to an ancestral state in an event called an evolutionary reversal. For example, the derived limbs of terrestrial tetrapods evolved from the ancestral fins of their aquatic ancestors. Then, within the mammals, the ancestors of modern cetaceans (whales and dolphins) returned to the ocean, and cetacean limbs evolved to once again resemble their ancestral state—fins. The superficial similarity of cetacean and fish fins does not suggest a close relationship between these groups. Instead, the similarity arises from evolutionary reversal.
In tracing the evolution of a character, biologists distinguish between ancestral and derived traits. Each character of an organism evolves from one condition (the ancestral trait) to another condition (the derived trait). Derived traits that are shared among a group of organisms and are also viewed as evidence of the common ancestry of the group are called synapomorphies (syn, "shared"; apo, "derived"; morph, "form," referring to the "form" of a trait). Thus the vertebral column is considered a synapomorphy—a shared, derived trait—of the vertebrates. (The ancestral trait was an undivided supporting rod.) Not all similar traits are evidence of relatedness. Similar traits in unrelated groups of organisms can develop for either of the following reasons:
As we noted earlier, any group of organisms that is treated as a unit in a biological classification system, such as all species in the genus Drosophila, or all insects, or all arthropods, is called a taxon. In the Linnaean system, species and genera are further grouped into a hierarchical system of higher taxonomic categories. The taxon above the genus in the Linnaean system is the family. The names of animal families end in the suffix "-idae." Thus Formicidae is the family that contains all ant species, and the family Hominidae contains humans and our recent fossil relatives, as well as our closest living relatives, the chimpanzees and gorillas. Family names are based on the name of a member genus; Formicidae is based on the genus Formica, and Hominidae is based on Homo. The same rules are used in classifying plants, except that the suffix "-aceae" is used for plant family names instead of "-idae." Thus Rosaceae is the family that includes the genus Rosa (roses) and its relatives. In the Linnaean system, families are grouped into orders, orders into classes, classes into phyla (singular phylum), and phyla into kingdoms. However, the ranking of taxa within Linnaean classification is subjective. Whether a particular taxon is considered, say, an order or a class is informative only with respect to the relative ranking of other related taxa. Although families are always grouped within orders, orders within classes, and so forth, there is nothing that makes a "family" in one group equivalent (in number of genera or in evolutionary age, for instance) to a "family" in another group. Linnaeus recognized the overarching hierarchy of life, but he developed his system before evolutionary thought had become widespread. Biologists today recognize the tree of life as the basis for biological classification and often name taxa without placing them into the various Linnaean ranks.
Linnaeus gave each species a two-part name, one part identifying the species itself and the other the genus to which it belongs. A genus (plural genera) is a group of closely related species. Optionally, the name of the taxonomist who first proposed the species name may be added at the end. Thus Homo sapiens Linnaeus is the name of the modern human species. Homo is the genus to which the species belongs, and sapiens identifies the particular species in the genus Homo; Linnaeus proposed the species name Homo sapiens. You can think of Homo as equivalent to your surname and sapiens as equivalent to your first name. The first letter of the genus name is capitalized, and the specific name is lowercase. Both of these formal designations are italicized. Rather than repeating the name of a genus when it is used several times in the same discussion, biologists often spell it out only once and abbreviate it to the initial letter thereafter (e.g., D. melanogaster rather than Drosophila melanogaster).
As biologists began to use DNA sequences to infer phylogenies in the 1970s and 1980s, they developed explicit mathematical models describing how DNA sequences change over time. These models account for multiple changes at a given position in a DNA sequence. They also take into account different rates of change at different positions in a gene, at different positions in a codon, and among different nucleotides. For example, transitions (changes between two purines or between two pyrimidines) are usually more likely than are transversions (changes between a purine and pyrimidine). Mathematical models can be used to compute how a tree might evolve given the observed data. A maximum likelihood method will identify the tree that most likely produced the observed data, given the assumed model of evolutionary change. Maximum likelihood methods can be used for any kind of characters, but they are most often used with molecular data, for which explicit mathematical models of evolutionary change are easier to develop. The principal advantages of maximum likelihood analyses are that they incorporate more information about evolutionary change than do parsimony methods, and they are easier to treat in a statistical framework. The principal disadvantages are that they are computationally intensive and require explicit models of evolutionary change (which may not be available for some kinds of character change).
MOLECULAR DATA All heritable variation is encoded in DNA, and so the complete genome of an organism contains an enormous set of traits (the individual nucleotide bases of DNA) that can be used in phylogenetic analyses. In recent years, DNA sequences have become among the most widely used sources of data for constructing phylogenetic trees. Comparisons of nucleotide sequences are not limited to the DNA in the cell nucleus. Eukaryotes have genes in their mitochondria as well as in their nuclei. Plant cells also have genes in their chloroplasts. The chloroplast genome (cpDNA), which is used extensively in phylogenetic studies of plants, has changed slowly over evolutionary time, so it is often used to study relatively ancient phylogenetic relationships. Most animal mitochondrial DNA (mtDNA) has changed more rapidly, so mitochondrial genes are used to study evolutionary relationships among closely related animal species (the mitochondrial genes of plants evolve more slowly). Many nuclear gene sequences are also commonly analyzed, and now that entire genomes have been sequenced from many species, they too are used to construct phylogenetic trees. Information on gene products (such as the amino acid sequences of proteins) is also widely used for phylogenetic analyses.
Reconstructing past events is important for understanding many biological processes. In the case of zoonotic diseases (diseases caused by infectious organisms transmitted to humans from another animal host), it is important to understand when, where, and how the disease first entered a human population. Human immunodeficiency virus (HIV) is the cause of such a zoonotic disease, acquired immunodeficiency syndrome, or AIDS. Phylogenetic analyses have become important for studying the transmission of viruses such as HIV. Phylogenies are also important for understanding the present global diversity of HIV and for determining the virus's origins in human populations. A broader phylogenetic analysis of immunodeficiency viruses shows that humans acquired these viruses from two different hosts: HIV-1 from chimpanzees, and HIV-2 from sooty mangabeys (Figure 21.7).
Phylogenetic trees can be constructed by using the parsimony principle to find the simplest explanation for phylogenetic data. Maximum likelihood methods incorporate more explicit mathematical models of evolutionary change to reconstruct evolutionary history.
Like most animals, flowering plants (angiosperms) often reproduce by mating with another individual of the same species. But in many angiosperm species, the same individual produces both male and female gametes (contained within pollen and ovules, respectively). *Self-incompatible species have mechanisms to prevent fertilization of the ovule by the individual's own pollen, and so must reproduce by outcrossing with another individual. Individuals of some species, however, regularly fertilize their ovules using their own pollen; they are self-fertilizing or selfing species, and their gametes are self-compatible.
The Origin of a Sexually Selected Trait The tail extension of male swordtails (genus Xiphophorus) apparently evolved through sexual selection, as females mated preferentially with males that had long "swords." Phylogenetic analysis reveals that Priapella split from the swordtails before the evolution of the sword. The independent finding that female Priapella prefer male Priapella with an artificial sword further supports the idea that this appendage evolved as a result of a preexisting preference in females.
Phylogenies enable biologists to compare organisms and make predictions and inferences based on similarities and differences in traits. Only homologous traits are used in reconstructing phylogenetic trees. A phylogenetic tree may portray the evolutionary history of all life forms. Phylogenetic trees can also depict the history of a major evolutionary group (such as the insects) or of a much smaller group of closely related species. In some cases, phylogenetic trees are used to show the history of individuals, populations, or genes within a species. The common ancestor of all the organisms in the tree forms the root of the tree.
We call a series of ancestor and descendant populations a lineage, which we can depict as a line drawn on a time axis, as shown in Figure 21.1. What happens when a single lineage divides into two? For example, a geographic barrier may divide an ancestral population into two descendant populations that no longer interbreed with one another. We depict such an event as a split, or node, in a phylogenetic tree (see Figure 21.1). Each of the descendant populations gives rise to a new lineage, and as these independent lineages evolve, new traits arise in each. As the lineages continue to split over time, this history can be represented in the form of a branching tree that can be used to trace the evolutionary relationships from the ancient common ancestor of a group of species, through the various lineage splits, up to the present populations of the organisms.
What are some reasons that similar traits might arise independently in species that are only distantly related? Can you think of examples among familiar organisms? How do biologists account for these homoplasies in reconstructing phylogenies? Selection for similar environmental conditions often leads to convergence in traits. For example, fish and dolphins both have fins and are similar in body shape because there is strong selection for these traits in an aquatic environment. But these traits have evolved independently in the two groups. Biologists can usually detect such homoplasies because they conflict with a large number of homologous traits in the groups that are similar as a result of their recent shared ancestry. Biologists can minimize homoplasies using the principle of parsimony.
Why is it important to consider only homologous characters in constructing phylogenetic trees? Because homologous characters are similar as a result of their common descent. Similarities that result from convergent evolution (the wings of birds and insects, for example) can be misleading about evolutionary relationships if they are mistaken as homologous characters.