Phylogenetics

Question 1

Phylogeny

Answer 1

Depicting the evolution of a lineage into branches

Question 2

Tips

Answer 2

the terminal end of an evolutionary tree, representing species, molecules, or populations being compared

Question 3

Branches

Answer 3

a lineage evolving through time that connects successive speciation or other branching events

Question 4

Nodes

Answer 4

a point in a phylogeny where a lineage splits (a speciation event or other branching event, such as the formation of subspecies)
internal nodes - a node that occurs within a phylogeny and represents ancestral populations or species

Question 5

Monophyletic

Answer 5

describes a group of organisms that form a clade

Question 6

Clade

Answer 6

a single “branch” in the tree of life; each clade represents an organism and all of its descendants

Question 7

Paraphyletic

Answer 7

describes a group of organisms that share a common ancestor, although the group does not include all the descendants of that common ancestor

Question 8

Outgroup

Answer 8

a group of organisms (for example, a species) that is outside of the monophyletic group being considered. In phylogenetic studies, outgroups can be used to infer the ancestral states of characters

Question 9

Taxon (taxa)

Answer 9

a group of organisms that a taxonomist judges to be a cohesive taxonomic unit, such as a species or order

Question 10

Most recent common ancestor (MRCA)

Answer 10

the most recent individual from which all the organisms of the set are descended

Question 11

Character

Answer 11

a heritable aspect of organisms that can be compared across taxa

Question 12

character state (ancestral state, derived state)

Answer 12

mutually exclusive features among taxa of a single paralog-equivalent assemblage that exhibit orthologous relationships to each other

Question 13

Synapomorphy

Answer 13

a derived form of a trait that is shared by a group of related species (that is, one that evolved in the immediate common ancestor of the group and was inherited by all of its descendants)

Question 14

Homoplasy

Answer 14

describes a character state similarity not due to shared descent (for example, produced by convergent evolution or evolutionary reversal

Question 15

Convergent evolution

Answer 15

the independent origin of similar traits in separate evolutionary lineages

Question 16

Evolutionary reversal (= character reversal)

Answer 16

the reversion of a derived character state to a form resembling its ancestral state

Question 17

Vestigial

Answer 17

the retention, during the process of evolution, of genetically determined structures or attributes that have lost some or all of the ancestral function in a given species

Question 18

Symplesiomorph

Answer 18

An ancestral character state (i.e., a plesiomorphy) shared by two or more lineages in a particular clade

Question 19

Homoplasy

Answer 19

When similar characteristics are not due to common ancestry, but instead arise by convergent evolution or evolutionary reversals (Homoplasy is common because there is only four possible character states)

Question 20

Reversal

Answer 20

ana ancestral trait that reappears in a lineage

Question 21

Slowly evolving characters

Answer 21

(include DNA sequences) can show the relationships between distantly related taxa

Question 22

Rapidly evolving characters

Answer 22

(including DNA sequence) can reveal relationships between closely related taxa

Question 23

How can DNA sequences be used to build phylogenetic trees?

Answer 23

• First align the DNA sequences from the species being examined so that the positions match eg. gene 1 is aligned with gene 1
• This is the character matrix. This matrix is no different than any other character matrix we’ve looked at, but instead of morphological traits, we have variation ata nucleotide position in the gene

Question 24

Neutral theory of molecular evolution

Answer 24

there are special types of DNA mutations that are not necessary favored or disfavored by natural selection

Question 25

Synonymous mutations

Answer 25

typically occur at a normal rate and behave like a clock

Question 26

Cladogram

Answer 26

shows branching order or topology only, the branch lengths do not mean anything

Question 27

Phylogram

Answer 27

a type of cladogram with branch lengths that reflect the amount of evolutionary change. Often this is derived from the number of mutations in DNA sequences

Question 28

Chronogram

Answer 28

a type of cladogram with branch lengths that are calibrated to real time; nodes indicate estimated ages of ancestors

Question 29

Symplesiomorphy

Answer 29

a shared ancestral character or trait

Question 30

Paraphyletic group

Answer 30

one that includes an ancestor and some, but not all, of its descendants

Question 31

Two ways to build trees

Answer 31

Morphological data
Molecular data