Chapter 20 Phylogeny

By applying a molecular clock, researchers have proposed that the first HIV-1 M invasion into humans occurred in the __________. 1830s 1890s 1930s 1950s 1980s

1930s *This is the point in time when some scientists estimate that HIV jumped from simians to humans.

CONCEPT 20.1 Phylogenies show evolutionary relationships (pp. 396-399)

> Linnaeus's binomial classification system gives organisms two part names: a genus plus a specific epithet. >> In the Linnaean system, species are grouped in increasingly broad taxa: Related genera are placed in the same family, families in orders, orders in classes, classes in phyla, phyla in kingdoms, and (more recently) kingdoms in domains. >>> Systematists depict evolutionary relationships as branching phylogenetic trees. Many systematists propose that classification be based entirely on evolutionary relationship >>>>Unless branch lengths are proportional to time or genetic change, a phylogenetic tree indicates only patterns of descent. >>>>> Much information can be learned about a species from its evolutionary history; hence, phylogenies are useful in a wide range of applications.

CONCEPT 20.2 Phylogenies are inferred from morphological and molecular data (pp. 399-400)

> Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with very different structures and genetic sequences. >> To infer phylogeny, homology (similarity due to shared ancestry) must be distinguished from analogy (similarity due to convergent evolution). >>>Computer programs are used to align comparable DNA sequences and to distinguish molecular homologies from coincidental matches between taxa that diverged long ago.

CONCEPT 20.3 Shared characters are used to construct phylogenetic trees (pp. 401-406)

>A clade is a monophyletic group that includes an ancestral species and all of its descendants. >>Clades can be distinguished by their shared derived characters. >>>Branch lengths can be proportional to amount of evolutionary change or time. t Among phylogenies, the most parsimonious tree is the one that requires the fewest evolutionary changes. >>>>Well-supported phylogenetic hypotheses are consistent with a wide range of data.

Sorting Homology from Analogy

>A potential source of confusion in constructing a phylogeny is similarity between organisms that is due to convergent evolution—called analogy—rather than to shared ancestry (homology). >>Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages >>>Analogous structures that arose independently are also called homoplasies (from the Greek, meaning "to mold in the same way"). >>>>The more elements that are similar in two complex structures, the more likely it is that the structures evolved from a common ancestor

maximum parsimony

>According to the principle of maximum parsimony, we should first investigate the simplest explanation that is consistent with the facts. >>(The parsimony principle is also called "Occam's razor")

Inferring Phylogenies Using Derived Characters Shared derived characters are unique to particular clades. Because all features of organisms arose at some point in the history of life, it should be possible to determine the clade in which each shared derived character first appeared and to use that information to infer evolutionary relationships.

>As a basis of comparison, we need to select an outgroup. >>An outgroup is a closely related species or group of species from a lineage that is known to have diverged before the lineage that includes the species we are studying (the ingroup). >>>A suitable outgroup can be determined based on evidence from morphology, paleontology, embryonic development, and gene sequences.

Shared Ancestral and Shared Derived Characters

>As a result of descent with modification, organisms have characteristics they share with their ancestors, and they also have characteristics that differ from those of their ancestors >>For example, all mammals have backbones, but a backbone does not distinguish mammals from other vertebrates because all vertebrates have backbones. The backbone predates the branching of mammals from other vertebrates. >>>Thus, for mammals, the backbone is a shared ancestral character, a character that originated in an ancestor of the taxon. >>>> In contrast, hair is a character shared by all mammals but not found in their ancestors. >>>>>Thus, in mammals, hair is considered a shared derived character, an evolutionary novelty unique to a clade.

What We Can and Cannot Learn from Phylogenetic Trees

>First, they are intended to show patterns of descent, not phenotypic similarity >>Second, the sequence of branching in a tree does not necessarily indicate the actual (absolute) ages of the particular species. >>>Third, we should not assume that a taxon on a phylogenetic tree evolved from the taxon next to it.

Hierarchical Classification

>In addition to naming species, Linnaeus also grouped them into a hierarchy of increasingly inclusive categories. The first grouping is built into the binomial: Species that appear to be closely related are grouped into the same genus >>Beyond genera, taxonomists employ progressively more comprehensive categories of classification. >>> The taxonomic system named after Linnaeus, the Linnaean system, places related genera into the same family, families into orders, orders into classes, classes into phyla (singular, phylum), phyla into kingdoms, and, more recently, kingdoms into domains >>>>The named taxonomic unit at any level of the hierarchy is called a taxon (plural, taxa)

Cladistics

>In the approach to systematics called cladistics, common ancestry is the primary criterion used to classify organisms. >>Using this methodology, biologists attempt to place species into groups called clades, each of which includes an ancestral species and all of its descendants >>>Clades, like taxonomic categories of the Linnaean system, are nested within larger clades. >>>>However, a taxon is equivalent to a clade only if it is monophyletic (from the Greek, meaning "single tribe"), signifying that it consists of an ancestral species and all of its descendants >>>>> Contrast this with a paraphyletic ("beside the tribe") group, which consists of an ancestral species and some, but not all, of its descendants , or a polyphyletic ("many tribes") group, which includes distantly related species but does not include their most recent common ancestor

CONCEPT 20.5 New information continues to revise our understanding of evolutionary history (pp. 408-410)

>Past classification systems have given way to the current view of the tree of life, which consists of three great domains: Bacteria, Archaea, and Eukarya. >>Phylogenies based in part on rRNA genes suggest that eukaryotes are most closely related to archaea, while data from some other genes suggest a closer relationship to bacteria. >>>Genetic analyses indicate that extensive horizontal gene transfer has occurred throughout the evolutionary history of life.

Morphological and Molecular Homologies

>Recall that phenotypic and genetic similarities due to shared ancestry are called homologies. **For example, the similarity in the number and arrangement of bones in the forelimbs of mammals is due to their descent from a common ancestor with the same bone structure; this is an example of a morphological homology (see Figure 19.16). >>In the same way, genes or other DNA sequences are homologous if they are descended from sequences carried by a common ancestor. >>>In general, organisms that share very similar morphologies or similar DNA sequences are likely to be more closely related than organisms with vastly different structures or sequences. >>>>In some cases, however, the morphological divergence between related species can be great and their genetic divergence small (or vice versa)

CONCEPT 20.4 Molecular clocks help track evolutionary time (pp. 406-408)

>Some regions of DNA change at a rate consistent enough to serve as a molecular clock, in which the amount of genetic change is used to estimate the date of past evolutionary events. Other DNA regions change in a less predictable way. >> Molecular clock analyses suggest that the most common strain of HIV jumped from primates to humans in the early 1900s.

Linking Classification and Phylogeny

>The evolutionary history of a group of organisms can be represented in a branching diagram called a phylogenetic tree. the branching pattern often matches how taxonomists have classified groups of organisms nested within more inclusive groups. >>Sometimes, however, taxonomists have placed a species within a genus (or other group) to which it is not most closely related. One reason for such a mistake might be that over the course of evolution, a species has lost a key feature shared by its close relatives >>> sister taxa, groups of organisms that share an immediate common ancestor and hence are each other's closest relatives. >>>>In addition, this tree, like most of the phylogenetic trees in this book, is rooted, which means that a branch point within the tree (often drawn farthest to the left) represents the most recent common ancestor of all taxa in the tree. The term basal taxon refers to a lineage that diverges from all other lineages in its group early in the history of the group >>>>>. Finally, on the lineage leading to taxa D-F, 5 represents a polytomy, a branch point from which more than two descendant groups emerge. A polytomy signifies that evolutionary relationships among the taxa are not yet clear.

Evaluating Molecular Homologies

>The first step after sequencing the DNA is to align comparable sequences from the species being studied. >>If the species are very closely related, the sequences probably differ at only one or a few sites. >>> In contrast, comparable nucleic acid sequences in distantly related species usually have different bases at many sites and may have different lengths. This is because insertions and deletions accumulate over long periods of time.

Phylogenetic Trees as Hypotheses

>This is a good place to reiterate that any phylogenetic tree represents a hypothesis about how the organisms in the tree are related to one another. >>The best hypothesis is the one that best fits all the available data. >>>A phylogenetic hypothesis may be modified when new evidence compels systematists to revise their trees.

Binomial Nomenclature

>To avoid ambiguity when communicating about their research, biologists refer to organisms by Latin scientific names. The two-part format of the scientific name, commonly called a binomial, was instituted in the 18th century by Carolus Linnaeus >>The first part of a binomial is the name of the genus (plural, genera) to which the species belongs. The second part, called the specific epithet, is unique for each species within the genus. An example of a binomial is Panthera pardus, the scientific name for the large cat commonly called the leopard

molecular clock

>the concept of a molecular clock, an approach for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates. >>An assumption underlying the molecular clock is that the number of nucleotide substitutions in related genes is proportional to the time that has elapsed since the genes branched from their common ancestor (divergence time).

What does a branch point in a phylogenetic tree represent? A branch point represents a gene duplication event. A branch point represents the absolute time at which two evolutionary lineages split from a common ancestor. A branch point represents a split between two phyla. A branch point represents a point at which two evolutionary lineages split from a common ancestor. A branch point represents a place where one species branches off from another.

A branch point represents a point at which two evolutionary lineages split from a common ancestor. *A branch point shows evolutionary relationships as a dichotomy.

A taxon __________.

A taxon is a formal grouping of organisms at any given level, such as species, genus, or phylum.

The two-part format of the scientific name, referred to as binomial, ensures that __________. each species has a name that is understandable regardless of language barriers among scientists systematists can easily specify the closest relatives of any species each species is assigned a unique name All of the listed responses are correct. None of the listed responses is correct

All of the listed responses are correct.

Which of the following best summarizes the neutral theory? Most harmful mutations are removed from a population quickly. Darwinian selection does not influence a lot of evolutionary change in genes and proteins because many of these changes do not affect fitness. Differences in the rate of the clock in different genes are a function of how important each gene is. If a particular sequence of amino acids is critical for survival, most new mutations will be harmful and fewer will be neutral. These genes will change slowly over time. Most mutations lead to dramatic changes in the evolution of a species

Darwinian selection does not influence a lot of evolutionary change in genes and proteins because many of these changes do not affect fitness. *Neutral theory states that these changes are mostly neutral, neither adaptive nor detrimental.

Universal phylogenetic trees built from different genes sometimes give inconsistent results. What basic assumption on which phylogenetic trees are based has probably been violated during the history of life? Genes are passed vertically from one generation to the next. Homologous traits come about because of common ancestry. The greater the difference in gene sequences, the longer two species have diverged. Analogous traits come about because of convergent evolution. Genes are often passed from one organism to another without the occurrence of reproduction.

Genes are passed vertically from one generation to the next. *Phylogenetic trees assume vertical gene transfer, but many organisms also use horizontal gene transfer. Many scientists postulate that horizontal gene transfer was far more prevalent during the early history of life.

The idea of using molecules as clocks to time evolutionary events is very attractive, but there are many problems in actually applying the technique. What seems to be the best way to get reliable results? It is best to use a gene that is essential to survival because they change more slowly. It is important to use one gene in which the changes are clearly neutral. It is important to use as many genes as possible. With this approach, fluctuations in evolutionary rate will tend to average out. It is important to use a gene that has been affected by natural selection to ensure that evolution will be observed. All of the listed responses are correct.

It is important to use as many genes as possible. With this approach, fluctuations in evolutionary rate will tend to average out. *It is almost impossible to find a gene that has been unaffected by natural selection during its entire existence. Using many genes has been shown to give dates that match the fossil record fairly closely.

To which domain is the domain Eukarya (the domain to which humans belong) most closely related? Fungi It is not clear whether eukaryotes are more closely related to bacteria or archaea. Archaea Bacteria Protista

It is not clear whether eukaryotes are more closely related to bacteria or archaea. *Studies of rRNA genes indicate that eukaryotes and archaea are more closely related, but genes that influence metabolism indicate a closer relationship between eukaryotes and bacteria. Horizontal gene transfer has likely been at work here.

Which statement below is true of parsimonious trees? The best tree requires the fewest evolutionary events to have occurred in the form of shared derived characters. Given the rules of how morphological traits change over time, a tree can be found that reflects the most likely sequence of evolutionary events. Trees can be constructed that are parsimonious or the most likely, but not both at the same time. Given the rules of how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events. The best tree requires the fewest evolutionary events to have occurred in the form of shared ancestral characters.

The best tree requires the fewest evolutionary events to have occurred in the form of shared derived characters. *This statement is true regarding trees based on morphological characters. For phylograms based on DNA, the most parsimonious tree requires the smallest number of base changes in DNA.

correct use of binomial nomenclature

The correct use of binomial nomenclature requires both genus and species, both italicized if typed or underlined if it is hand-written. Genus is always written first and the first letter capitalized and species is always the second word and is lowercase.

Birds and mammals have a four-chambered heart, but most reptiles have a three-chambered heart. How does this fact affect the construction of phylogenetic trees for these groups? This represents a problem with the principle of parsimony, rather than a problem with the analogy-homology issue. The most likely tree is not always the most parsimonious. The most likely tree is always the most parsimonious. It shows that the common ancestor of birds and mammals must have had a four-chambered heart. None of the listed responses is correct.

The most likely tree is not always the most parsimonious. *Evidence shows that birds diverged from reptiles before mammals did; therefore, there is no common ancestor of birds and mammals that had a four-chambered heart. This character must have evolved twice.

Which statement below is true about an outgroup? Outgroup comparison is based on the assumption that homologies present in both the outgroup and ingroup must be derived characters. The outgroup and ingroup display a mixture of shared and derived characters. The outgroup should be less closely related to any members of the ingroup than they are to each other. The outgroup would be found at one of the highest branches of a phylogenetic tree. None of the listed responses is correct.

The outgroup should be less closely related to any members of the ingroup than they are to each other. *The outgroup should be known to be less closely related than any ingroup members are to each other based on other evidence such as paleontology, embryonic development, and gene sequences.

From Two Kingdoms to Three Domains

The three domains—Bacteria, Archaea, and Eukarya—are a taxonomic level higher than the kingdom level. >The domain Bacteria contains most of the currently known prokaryotes, >>while the domain Archaea consists of a diverse group of prokaryotic organisms that inhabit a wide variety of environments. >>>The domain Eukarya consists of all the organisms that have cells containing true nuclei. This domain includes many groups of single-celled organisms as well as multicellular plants, fungi, and animals

Phylogeny

To help make sense of that diversity, biologists trace ___________the evolutionary history of a species or group of species.

The wings of a hummingbird and a bee are __________. phylogenetic homologous analogous binomial taxonomic

analogous *Structures that are similar as a result of convergent evolution are referred to as analogous structures.

Which of the following would be the LEAST useful in determining the relationships among various species? amino acid sequences of proteins homologous structures a comparison of DNA base sequences analogous structures fossils

analogous structures *Analogous structures are the result of convergent evolution and may not reflect the relationships among the species that share them.

Which of the following methods to establish phylogenetic relationships among organisms has been developed most recently? comparing physiology (the functioning of structures and systems) comparing behavioral patterns comparing the component sequences of proteins and nucleic acids comparing embryonic development comparing morphology (shape and structure)

comparing the component sequences of proteins and nucleic acids *The comparison of nucleic acids and proteins has become a powerful addition to the other comparative methods that systematists use to measure evolutionary relationships among species.

A phylogenetic tree of bird families constructed by cladistic analysis would be a hypothesis about which of the following? families that look most alike characteristics shared by all bird families analogous structures shared by various species relative ages of living species of birds evolutionary relationships among bird families

evolutionary relationships among bird families *Phylogenetic trees are constructed to reflect the evolutionary relationships among organisms.

The binomial system assigns to each organism a unique name that describes its __________. order and family body plan and habitat family and species genus and species evolutionary history

genus and species *Each species is assigned a two-part Latin name, or binomial. The first word is the genus and the second word is the species. Species that are very similar are grouped into the same genus.

Rabbits and guinea pigs both belong to Class Mammalia. This means they must also both belong to __________. family Caviidae order Rodentia phylum Chordata genus Cavia All of the listed responses are correct.

phylum Chordata Class is less inclusive than phylum; organisms that are in the same class are also in the same phylum

Unlike a regular phylogenetic tree, phylogenetic trees with branch lengths proportional to time can be used to __________. represent the chronological time that has passed since two groups diverged from a common ancestor reflect the rate of evolutionary change reflect the number of evolutionary changes that have taken place in a lineage hypothesize the relative relatedness between different taxa tie polyphyletic clades to a common ancestor

represent the chronological time that has passed since two groups diverged from a common ancestor *In this type of tree, called an ultrametric tree, the branching pattern is the same as in a normal phylogenetic tree, but all the branches that can be traced from the common ancestor to the present are of equal length.

There are three different species: A, B, & C. Species A and species B are in the same phylum. Species A and species C are in the same order. From this information you can conclude that __________. SHOW HINT species B and species C share a less recent ancestor than do species A and B all three species are not members of the same phylum species A and species B are in the same family species C could be in the same class as species A and B all three species are members of the same genus

species C could be in the same class as species A and B *If species A and species C are in the same order, then they must also be in the same class. Because you know that species A and species B are in the same phylum, it is possible that they are in the same class, but different orders.

In this chapter, we'll examine how biologists reconstruct and interpret phylogenies using ,__________ a discipline focused on classifying organisms and determining their evolutionary relationships.

systematics

A discipline that is focused on classifying organisms and determining their evolutionary relationships is __________. binomial nomenclature evolution systematics phylogeny taxonomy

systematics *Systematists study morphological and behavioral resemblances as well as molecular similarities and differences to devise theories about relationships.

how organisms are named and classified, the scientific discipline of ______

taxonomy

What is the focus of the branch of biology called taxonomy? genetics the classification of life-forms by their similarities and differences the history of the field of biology the environment evolution

the classification of life-forms by their similarities and differences *

Using cladistic analysis, a taxonomist wishes to construct a phylogenetic tree showing the relationships among various species of mammals. Which of the following would be the LEAST useful for this purpose? the fact that teeth vary among types of mammals the fact that all mammals have hair descriptions of various types of limbs (wings, legs, flippers, etc.) DNA base sequences data about skull bones

the fact that all mammals have hair *As a shared derived character, hair cannot be used to determine the phylogeny of mammals.