Chapter 26: Phylogeny

Question 1

Horizontal gene transfer

Answer 1

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

Question 2

Taxonomy

Answer 2

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

Question 3

Parallelism (homoplasy)

Answer 3

An instance of two taxa sharing a derived trait while lacking an immediately recent ancestor ommon to them both.

Question 4

Paraphyletic group

Answer 4

An invalid clade where at least one taxon is missing.

Question 5

Clade

Answer 5

A group of taxa that includes an ancestor and all of its descendants.

Question 6

Transition

Answer 6

DNA substitution mutation wherein purines are interchanged with purines and pyrimadines with pyrimadines.

Question 7

Homology

Answer 7

An instance of a trait being present in both an ancestor and its descendants.

Question 8

Phylogeny

Answer 8

The evolutionary history of a species or a group of related species.

Question 9

Sister taxa

Answer 9

Two taxa that share an immediate common ancestor.

Question 10

Polyphyletic group

Answer 10

An invalid clade where the common ancestor is missing.

Question 11

Neutral theory

Answer 11

The theory that most evolutionary change in genes and proteins has no effect on fitness and is not enfluenced by natural selection.

Question 12

Polytomy

Answer 12

An instance of unresolved phylogeny wherein a branch point diverges into more than two taxa.

Question 13

Transversion

Answer 13

DNA substitution mutation wherein purines are interchanged with pyrimadines.

Question 14

Maximum likelihood

Answer 14

A principle applied to DNA sequence data 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 15

Orthologous gene

Answer 15

Homologous genes that are found in different species because of speciation.

Question 16

Synapomorphy

Answer 16

An instance of a shared derived character that is an evolutionary novelty unique to a particular clade.

Question 17

Outgroup

Answer 17

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; this group 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 18

Character matrix

Answer 18

A matrix that maps traits against taxa. This matrix is often binary, indicating the presence or absence of a trait.

Question 19

Nested taxonomy

Answer 19

The system of supergroups and subgroups applied to standard taxonomy.

Question 20

Phylogenetic tree

Answer 20

A branched mapping of hypothetical evolutionary relationships.

Question 21

Plesiomorphy

Answer 21

An instance of a shared character that originated in an ancestral taxon.

Question 22

Paralogous gene

Answer 22

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

Question 23

Cladistics

Answer 23

The system of grouping organisms by common descent.

Question 24

Basal taxon

Answer 24

The null taxon that diverged at the beginning of a particular phylogenetic tree, branching off at the last common ancestor.

Question 25

Reversal (homoplasy)

Answer 25

An instance of a trait shared between an ancestor and one of its distant descendants that is not present in intermediate descendants.

Question 26

Maximum parsimony

Answer 26

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

Question 27

Molecular clock

Answer 27

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 28

Branch point

Answer 28

The intersection of two branches on a phylogenetic tree, indicating where two taxa have diverged from their common ancestor.

Question 29

Polymerase chain reaction

Answer 29

A technique for amplifying DNA in vitro by incubating it with specific primers, a heat-resistant DNA polymerase, and nucleotides.

Question 30

Taxon

Answer 30

A taxonomic unit at any given level of classification.

Question 31

Monophyletic group

Answer 31

A valid clade, i.e. a group that includes an ancestor and all of its descendants.

Question 32

Gene family

Answer 32

A group of related genes within an organism’s genome.

Question 33

Ingroup

Answer 33

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

Question 34

Systematics

Answer 34

A scientific discipline focused on classifying organisms and determining their evolutionary relationships.

Question 35

Rooted tree

Answer 35

A phylogenetic tree that includes a single ancestral branch at one end to indicate the last common ancestor of all taxa on the tree.