26. Phylogeny and the tree of life

Question 1

Key concepts

Answer 1

26.1 Phylogenies show evolutionary relationships
26.2 Phylogenies are inferred from morphological and molecular data
26.3 Shared characters are used to construct phylogenetic trees
26.4 An organism’s evolutionary history is documented in its genome
26.5 Molecular clocks help track evolutionary time
26.6 Our understanding of the tree of life continues to change based on new data

Question 2

phylogeny

Answer 2

The evolutionary history of a species or group of related species

Question 3

systematics

Answer 3

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

Question 4

binomial

Answer 4

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

Question 5

genus

Answer 5

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

Question 6

Hierarchical classification

Answer 6

genus, family, orders, classes, phyla, kingdoms, domains

Question 7

phylogenetic tree

Answer 7

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

Question 8

branch point

Answer 8

the representation of 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

Question 9

evolutionary lineage

Answer 9

the sequence of ancestral organisms leading to a particular taxon; represented by a branch (line) in a phylogenetic tree

Question 10

sister taxa

Answer 10

groups of organisms that share an immediate common ancestor and hence are each other’s closest relatives

Question 11

rooted phylogenetic tree

Answer 11

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

Question 12

basal taxon

Answer 12

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

Question 13

homologies

Answer 13

similarity in characteristics resulting from a shared ancestry

Question 14

analogy

Answer 14

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

Question 15

cladistics

Answer 15

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

Question 16

clades

Answer 16

a group of species that includes an ancestral species and all of its descendants. A clade is equivalent to a monophyletic group.

Question 17

monophyletic

Answer 17

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.

Question 18

paraphyletic

Answer 18

pertaining to a group of taxa that consists of a common ancestor and some but not all, of its descendants

Question 19

polyphyletic

Answer 19

pertaining to a group of taxa that includes distantly related organisms but does not include their most recent common ancestor

Question 20

shared ancestral character

Answer 20

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

Question 21

shared derived character

Answer 21

an evolutionary novelty that is unique to a particular clade

Question 22

outgroup

Answer 22

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

Question 23

ingroup

Answer 23

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

Question 24

maximum parsimony

Answer 24

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

Question 25

maximum likelihood

Answer 25

as applied to DNA sequence data, a principle that states that when considering multiple phylogenetic hypotheses one should take into account the hypothesis that reflects the most likely sequence of evolutionary events given certain rules about how DNA changes over time

Question 26

orthologous genes

Answer 26

• homologous genes that are found in different species because of speciation

Question 27

paralogous genes

Answer 27

homologous genes that are found in the same genome as a result of gene duplication

Question 28

molecular clock

Answer 28

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

Question 29

horizontal gene transfer

Answer 29

the transfer of genes from one genome to other through mechanisms such as transposable elements, plasmid exchange, viral activity and perhaps fusions of different organisms

Question 30

Concept 26 summary

Answer 30

• 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.

Question 31

Concept 26.2 summary

Answer 31

• 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 32

Concept 26.3 summary

Answer 32

• 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.
  -Among phylogenies, the most parsimonious tree is the one that requires the fewest evolutionary changes. The most likely tree is the one based on the most likely pattern of changes.
  -Well-supported phylogenetic hypotheses are consistent with a wide range of data.

Question 33

Concept 26.4 summary

Answer 33

• Orthologous genes are homologous genes found in different species as a result of speciation. Paralogous genes are homologous genes within a species that result from gene duplication; such genes can diverge and potentially take on new functions.
  -Distantly related species often have many orthologous genes. The small variation in gene number in organisms of varying complexity suggests that genes are versatile and may have multiple functions.

Question 34

Concept 26.5 summary

Answer 34

• Some regions of DNA change at a rate consistent enough to serve as a molecular clock, a method of estimating the date of past evolutionary events based on the amount of genetic change. 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.

Question 35

Concept 26.6 summary

Answer 35

• 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.

Question 36

In a cladistic approach to systematics, an outgroup is

Answer 36

a species or group of species from an evolutionary lineage that is known to have diverged before the lineage that includes all the species under study

Question 37

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?

Answer 37

The most likely tree is not always the most parsimonious.

Question 38

In cladistics, biologists attempt to place species into groups that each include an ancestral species and all of its descendants. A group that is paraphyletic fails to accomplish this goal in what way?

Answer 38

It consists of an ancestral species and some, but not all, of its descendants.

Question 39

By applying a molecular clock, researchers have proposed that the first HIV-1 M invasion into humans occurred in the

Answer 39

1930s

Question 40

Which of the following is a true statement concerning horizontal gene transfer?

Answer 40

Horizontal gene transfer is known to occur within both prokaryotes and eukaryotes.

Question 41

Why are phylogenetic trees considered hypotheses?

Answer 41

A phylogenetic tree can be used to make testable predictions.

Question 42

The binomial system assigns to each organism a unique name that describes its __________.

Answer 42

genus and species

Question 43

Rabbits and guinea pigs both belong to class Mammalia. This means they must also both belong to __________.

Answer 43

phylum Chordata

Question 44

A bald eagle and a black bear both have four limbs with digits because they are both tetrapods, descendants of a four-limbed ancestor. In this comparison, the limbs of the eagle and the bear are what type of structure?

Answer 44

Homologous

Question 45

A taxon

Answer 45

is a formal grouping at any given level

Question 46

Which of the following is the correct order of taxonomic levels in the Linnean system of classification, from most to least inclusive?

Answer 46

Domain, kingdom, phylum, class, order, family, genus, species

Question 47

What is the basis for the use of a molecular clock to determine the absolute time of evolutionary change?

Answer 47

Nucleotide substitutions in a gene occur at a relatively constant rate.

Question 48

The separate lineages leading to dolphins and sharks both evolved streamlined bodies, dorsal fins, and broad tail fins as adaptations to efficient locomotion in a marine environment. In this comparison, the bodies and fins of dolphins and sharks are what type of structures?

Answer 48

analogous

Question 49

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 __________.

Answer 49

a paraphyletic group

Question 50

Sister taxa on a phylogenetic tree are defined as groups that __________.

Answer 50

share an immediate common ancestor and are each other’s closest relatives

Question 51

The principle of maximum parsimony is applied to the process of constructing a phylogenetic tree in what way?

Answer 51

The tree that requires the fewest evolutionary events, as measured by the origin of shared derived characters, is selected.

Question 52

Two genes are recognized as orthologous if

Answer 52

they are homologous genes found in different species, and their divergence traces back to speciation events that produced the species

Question 53

The term polytomy refers to a situation in which __________.

Answer 53

there is a branch point on a phylogeny from which more than two descendent groups emerge

Question 54

Researchers can use molecular homologies to __________.

Answer 54

reveal the number of mutations in a particular sequence that has occurred in each species since they diverged from a common ancestor

Question 55

Which of the following would be the least useful in determining the relationships among various species?

Answer 55

Analogous structures

Question 56

What is a primary reason why a three-domain taxonomic scheme has been adopted over the previous five-kingdom taxonomic scheme?

Answer 56

Phylogenies based on genetic data revealed that some prokaryotes (kingdom Monera) differ as much from each other as they differ from eukaryotes.

Question 57

If you wanted to determine the lineage of plants that have evolved on a relatively young archipelago—approximately 15,000 years old—what type of nucleic acid should you compare?

Answer 57

mtDNA

Question 58

A phylogenetic tree of bird families constructed by cladistic analysis would be a hypothesis about which of the following?

Answer 58

Evolutionary relationships among bird families

Question 59

Which of the following best summarizes the neutral theory?

Answer 59

Darwinian selection does not influence a lot of evolutionary change in genes and proteins because many of these changes do not affect fitness.

Question 60

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?

Answer 60

It is important to use as many genes as possible. With this approach, fluctuations in evolutionary rate will tend to average out.

Question 61

What is the relationship between systematics and taxonomy?

Answer 61

Systematics is a discipline within taxonomy.