Biology 111G Chapter 20 concept checks and end of chapter review

Shared derived character

An evolutionary novelty that is unique to a particular clade

homologies

Recall that phenotypic and genetic similarities due to shared ancestry

Concept 20.4: Molecular clocks help track evolutionary time

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.

WHAT IF? Suppose that two species, A and B, have similar appearances but very divergent gene sequences, while species B and C have very different appearances but similar gene sequences. Which pair of species is more likely to be closely related: A and B, or B and C? Explain.

Species B and C are more likely to be closely related. Small genetic changes (as between species B and C) can produce divergent physical appearances, but if many genes have diverged greatly (as in species A and B), then the lineages have probably been separate for a long time.

Which levels of the classification in Figure 20.3 do humans share with leopards?

We are classified the same from the domain level to the class level; both the leopard and human are mammals. Leopards belong to order Carnivora, whereas humans do not.

phylogenetic tree.

a branching diagram that represents a hypothesis about the evolutionary history of a group of organisms.

systematics,

a discipline focused on classifying organisms and determining their evolutionary relationships.

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

analogy

similarity between two species that is due to convergent evolution rather than to descent from a common ancestor with the same trait

example of a morphological homology

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

clades

A group of species that includes an ancestral species and all its descendants.

molecular clock

A method for estimating the time required for a given amount of evolutionary change, based on the observation that some regions of genomes evolve at constant rates.

What is a molecular clock? What assumption underlies the use of a molecular clock?

A molecular clock is a method of estimating the actual time of evolutionary events based on numbers of base changes in genes that are related by descent. It is based on the assumption that the regions of genomes being compared evolve at constant rates.

cladistics

An approach to systematics in which organisms are placed into groups called clades based primarily on common descent.

In Figure 20.4, which similarly inclusive taxon descended from the same common ancestor as Canidae? A-Felidae B-Mustelidae C-Carnivora D-Lutra

B-Mustelidae

Explain why phylogenies based on different genes can yield different branching patterns for the tree of all life.

Because of horizontal gene transfer, some genes in eukaryotes are more closely related to bacteria, while others are more closely related to archaea; thus, depending on which genes are used, phylogenetic trees constructed from DNA data can yield conflicting results.

rooted

Describing a phylogenetic tree that contains a branch point (often, the one farthest to the left) representing the most recent common ancestor of all taxa in the tree.

To distinguish a particular clade of mammals within the larger clade that corresponds to class Mammalia, would hair be a useful character? Why or why not?

No; hair is a shared ancestral character common to all mammals and thus is not helpful in distinguishing different mammalian subgroups.

Concept 20.5: New information continues to revise our understanding of evolutionary history

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.

paraphyletic

("beside the tribe") Pertaining to a group of taxa that consists of a common ancestor and some, but not all, of its descendants.

polyphyletic

("many tribes") Pertaining to a group of taxa that includes distantly related organisms but does not include their most recent common ancestor.

Decide whether each of the following pairs of structures more likely represents analogy or homology, and explain your reasoning: (a) a porcupine's quills and a cactus's spines; (b) a cat's paw and a human's hand; (c) an owl's wing and a hornet's wing.

(a) Analogy, since porcupines and cacti are not closely related and since most other animals and plants do not have similar structures; (b) homology, since cats and humans are both mammals and have homologous forelimbs, of which the hand and paw are the lower part; (c) analogy, since owls and hornets are not closely related and since the structure of their wings is very different

monophyletic

(from the Greek, meaning "single tribe"), pertaining to a group of taxa that consists of a common ancestor and all of its descendants. A monophyletic taxon is equivalent to a clade.

homoplasies

(from the Greek, meaning "to mold in the same way"). A similar analogous structure or molecular sequence that has evolved independently in two species.

Question: Humans and chimpanzees are sister species. Explain what that means.

20.1 The fact that humans and chimpanzees are sister species indicates that we share a more recent common ancestor with chimpanzees than we do with any other living primate species. But that does not mean that humans evolved from chimpanzees, or vice versa; instead, it indicates that both humans and chimpanzees are descendants of that common ancestor.

Question: Why is it necessary to distinguish homology from analogy to infer phylogeny?

20.2 Homologous characters result from shared ancestry. As organisms diverge over time, some of their homologous characters will also diverge. The homologous characters of organisms that diverged long ago typically differ more than do the homologous characters of organisms that diverged more recently. As a result, differences in homologous characters can be used to infer phylogeny. In contrast, analogous characters result from convergent evolution, not shared ancestry, and hence can give misleading estimates of phylogeny.

Question: Describe some assumptions and limitations of molecular clocks.

20.4 A key assumption of molecular clocks is that nucleotide substitutions occur at fixed rates, and hence the number of nucleotide differences between two DNA sequences is proportional to the time since the sequences diverged from each other. Some limitations of molecular clocks: No gene marks time with complete precision; natural selection can favor certain DNA changes over others; nucleotide substitution rates can change over long periods of time (causing molecular clock estimates of when events in the distant past occurred to be highly uncertain); and the same gene can evolve at different rates in different organisms.

Question: Why was the five-kingdom system abandoned for a three-domain system?

20.5 Genetic data indicated that many prokaryotes differed as much from each other as they did from eukaryotes. This indicated that organisms should be grouped into three "super-kingdoms," or domains (Archaea, Bacteria, Eukarya). These data also indicated that the previous kingdom Monera (which had contained all the prokaryotes) did not make biological sense and should be abandoned. Later genetic and morphological data also indicated that the former kingdom Protista (which had primarily contained single-celled organisms) should be abandoned because some protists are more closely related to plants, fungi, or animals than they are to other protists.

Genes are sequences of thousands of nucleotides, each of which represents an inherited character in the form of one of the four DNA bases:

A (adenine), G (guanine), C (cytosine), or T (thymine).

shared ancestral character,

A character that is shared by members of a particular clade but that originated in an ancestor that is not a member of that clade

Concept 20.3: Shared characters are used to construct phylogenetic trees

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. 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.

binomial,

A common term for the two-part, latinized format for naming a species, consisting of the genus and specific epithet; also called a binomen.

Maximum Parsimony (Occam's Razor)

A principle that states that when considering multiple explanations for an observation, one should first investigate the simplest explanation that is consistent with the facts.

taxonomy.

A scientific discipline concerned with naming and classifying the diverse forms of life

genus

A taxonomic category above the species level, designated by the first word of a species' two-part scientific name.

In a comparison of birds and mammals, the condition of having four limbs is A-a shared ancestral character. B-a shared derived character. C-a character useful for distinguishing birds from mammals. D-an example of analogy rather than homology.

A-a shared ancestral character.

If you were using cladistics to build a phylogenetic tree of cats, which of the following would be the best outgroup? A-wolf B-domestic cat C-frog D-leopard

A-wolf

To apply parsimony to constructing a phylogenetic tree, A-choose the tree that assumes all evolutionary changes are equally probable. B-choose the tree in which the branch points are based on as many shared derived characters as possible. C-choose the tree that represents the fewest evolutionary changes, in either DNA sequences or morphology. D-choose the tree with the fewest branch points.

C-choose the tree that represents the fewest evolutionary changes, in either DNA sequences or morphology.

Three living species X, Y, and Z share a common ancestor T, as do extinct species U and V. A grouping that consists of species T, X, Y, and Z (but not U or V) makes up A- a monophyletic taxon. B- an ingroup, with species U as the outgroup. C-a polyphyletic group. D- a paraphyletic group.

D- a paraphyletic group.

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.

polytomy

In a phylogenetic tree, a branch point from which more than two descendant taxa emerge. A polytomy indicates that the evolutionary relationships between the descendant taxa are not yet clear.

Concept 20.1: Phylogenies show evolutionary relationships

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 relationships. 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

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.

Question: What does this phylogenetic tree indicate about the evolutionary relationships between the leopard, badger, and wolf?

The branching pattern of the tree indicates that the badger and the wolf share a common ancestor that is more recent than the ancestor these two animals share with the leopard.

WHAT IF? Draw the three possible dichotomously branching trees showing evolutionary relationships for the domains Bacteria, Archaea, and Eukarya. Two of these trees have been supported by genetic data. Is it likely that the third tree might also receive such support? Explain your answer.

The fossil record indicates that prokaryotes originated long before eukaryotes. This suggests that the third tree, in which the eukaryotic lineage diverged first, is not accurate and hence is not likely to receive support from genetic data.

WHAT IF? Suppose a molecular clock dates the divergence of two taxa at 80 million years ago, but new fossil evidence shows that the taxa diverged at least 120 million years ago. Explain how this could happen.

The gene (or genes) used for the molecular clock may have evolved more slowly in these two taxa than in the species used to calibrate the clock; as a result, the clock would underestimate the time at which the taxa diverged from each other.

Why is the kingdom Monera no longer considered a valid taxon?

The kingdom Monera included bacteria and archaea, but we now know that these organisms are in separate domains. Kingdoms are subsets of domains, so a single kingdom (like Monera) that includes taxa from different domains is not valid.

The most parsimonious tree of evolutionary relationships can be inaccurate. How can this occur?

The principle of maximum parsimony states that the hypothesis about nature we investigate first should be the simplest explanation found to be consistent with the facts. Actual evolutionary relationships may differ from those inferred by parsimony owing to complicating factors such as convergent evolution.

branch points

The representation on a phylogenetic tree of the divergence of two or more taxa from a common ancestor. A branch point is usually shown as a dichotomy in which a branch representing the ancestral lineage splits (at the branch point) into two branches, one for each of the two descendant lineages.

WHAT IF? Draw a phylogenetic tree that includes the relationships from Figure 20.16 and those shown here. Traditionally, all the taxa shown besides birds and mammals were classified as reptiles. Would a cladistic approach support that classification? Explain.

The traditional classification provides a poor match to evolutionary history, thus violating the basic principle of cladistics—that classification should be based on common descent. Both birds and mammals originated from groups traditionally designated as reptiles, making reptiles (as traditionally delineated) a paraphyletic group. These problems can be addressed by removing Dimetrodon and cynodonts from the reptiles and by regarding birds as a group of reptiles (specifically, as a group of dinosaurs).

horizontal gene transfer,

The transfer of genes from one genome to another through mechanisms sucks as transposable elements, plasmid exchange, viral activity and perhaps fusions of different organisms.

Which of the trees shown here depicts an evolutionary history different from the other two? Explain.

The tree in (c) shows a different pattern of evolutionary relationships. In (c), C and B are sister taxa, whereas C and D are sister taxa in (a) and (b).

Question: Why might you expect organisms that are not closely related to nevertheless share roughly 25% of their bases?

There are four possible bases (A, C, G, T) at each nucleotide position. If the base at each position depends on chance, not common descent, we would expect roughly one out of four (25%) of them to be the same.

Then explain how numerous base changes could occur in an organism's DNA yet have no effect on its survival and reproduction.

There are many portions of the genome that do not code for genes; mutations that alter the sequence of bases in such regions could accumulate without affecting an organism's survival and reproduction. Even in coding regions of the genome, some mutations may not have a critical effect on genes or proteins.

Taxon

a named taxonomic unit at any given level of classification

outgroup

a species or group of species from an evolutionary lineage that is known to have diverged before the lineage that contains the group of species being studied. An outgroup is selected so that its members are closely related to the group of species being studied, but not as closely related as any study-group members are to each other

ingroup

a species or group of species whos evolutionary relationships are being examined in a given analysis.

basal taxon

in a specified group of organisms, a taxon whose evolutionary lineage diverged early in the history of the group.

the specific epithet

is unique for each species within the genus.

Convergent evolution

occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages.

clue to distinguishing between homology and analogy

the complexity of the characters being compared.

phylogeny

the evolutionary history of a species or group of species.

phylogenetic bracketing

we can predict (by parsimony) that features shared by two groups of closely related organisms are present in their common ancestor and all of its descendants unless independent data indicate otherwise.