Lab 3: Constructing a Phylogenetic Tree

Question 1

Phylogenetics

Answer 1

Phylogenetics is the study of evolutionary relationships among groups of organisms (e.g. species, populations), which are discovered through molecular sequencing data and morphological data matrices.

Question 2

Phylogeny

Answer 2

the branch of biology that deals with phylogenesis;
another term for phylogenesis.

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

Question 3

Cladistics

Answer 3

a method of classification of animals and plants according to the proportion of measurable characteristics that they have in common. It is assumed that the higher the proportion of characteristics that two organisms share, the more recently they diverged from a common ancestor.

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

Question 4

Apomorphy

Answer 4

a new or descendant character state

An apomorphy (“separate form”) or derived state is an innovation. It can thus be used to diagnose a clade – or even to help define a clade name in phylogenetic nomenclature.

Question 5

Synapomorphy

Answer 5

the possession by two organisms of an apomorphy, a characteristic (not necessarily the same in each) that is derived from one characteristic in an organism from which they both evolved.

Used to infer phylogenetic relationships.

On phylogenetic trees, they are usually denoted with hash lines and numbers like: 2(1)

Question 6

Symplesiomorphy

Answer 6

In cladistics, a symplesiomorphy or symplesiomorphic character is an ancestral trait shared by two or more taxa. A plesiomorphy refers to the ancestral trait on its own, usually in reference to another, more derived trait.

Question 7

plesiomorphy

Answer 7

A plesiomorphy refers to the ancestral trait on its own, usually in reference to another, more derived trait.
A symplesiomorphic trait is also shared with other taxa that have an earlier last common ancestor with the taxa under consideration.

These characters don’t help resolve phylogenetic relationships

Question 8

phylogenesis

Answer 8

the evolutionary development and diversification of a species or group of organisms, or of a particular feature of an organism.

Question 9

parsimony

Answer 9

Refers to a rule used to choose among possible cladograms, which states that the cladogram implying the least number of changes in character states is the best.

The parsimony principle is basic to all science and tells us to choose the simplest scientific explanation that fits the evidence. In terms of tree-building, that means that, all other things being equal, the best hypothesis is the one that requires the fewest evolutionary changes.

Question 10

monophyletic

Answer 10

(of a group of organisms) descended from a common evolutionary ancestor or ancestral group, esp. one not shared with any other group.

All members of the group and all descendant share the same most recent ancestor.

Question 11

paraphyletic

Answer 11

(of a group of organisms) descended from a common evolutionary ancestor or ancestral group, but not including all the descendant groups.

Question 12

polyphyletic

Answer 12

(of a group of organisms) derived from more than one common evolutionary ancestor or ancestral group and therefore not suitable for placing in the same taxon.

Question 13

homology

Answer 13

Similarity in characteristics resulting from a shared ancestry.

Question 14

homologous structures

Answer 14

Structures in different species that are similar because of common ancestry. 2 or more structures that all are derived from one structure in a common ancestor.

Question 15

homoplasy

Answer 15

A similar (analogous) structure or molecular sequence that has evolved independently in two species.

Creates analogous structures that have similar form or function, but were not present in the last common ancestor of those groups. The cladistic term for the same phenomenon is homoplasy, (from Greek for same form). The recurrent evolution of flight is a classic example of convergent evolution. Flying insects, birds, and bats have all evolved the capacity of flight independently. They have “converged” on this useful trait.

On phylogenic trees, analogous structures are denoted by an asterisk (*).

Question 16

Unmodified trait

Answer 16

Ancestral

Question 17

Modified

Answer 17

Derived

Question 18

4 Steps to Constructing a Phylogeny

Answer 18

1. Identify potential homologous characters.
2. Designate a group to determine the order and polarity of the characters (which ones are ancestral, and which are derived).
3. Code the characters and construct a matrix.
4. Group by synapomorphies: analyze the matrix to produce a phylogenetic hypothesis.

Question 19

character

Answer 19

An observable heritable trait that may vary among individuals.

May be morphological, physiological, behavioral, molecular, or ecological.

May be passed down in a modified or unmodified character state.

Question 20

Example of Homology:

Vertebrate Forelimb

Answer 20

The basic fore limb plan is retained throughout the vertebrates: There is a humerus, a radius & ulna, carpals, metacarpals, digits comprising phalanges.

Frogs & Birds have variants of fused parts.

Question 21

apo-

Answer 21

derived

Question 22

-morphy

Answer 22

form

Question 23

syn-

Answer 23

shared

Question 24

outgroup

Answer 24

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 25

ingroup

Answer 25

A species or group of species whose evolutionary relationships we seek to determine.

Question 26

Clade

Answer 26

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

Question 27

node

Answer 27

Represents a speciation event. It’s a point of divergence.

Question 28

Outgroup Comparison

Answer 28

Typically, the ancestral trait is coded “0,” and derived traits are coded “1,” “2,” “3,” etc.

Question 29

multistate character

Answer 29

A character that can occur in several character states. Often encoded 0,1,2,3…

Question 30

Binary characters

Answer 30

Exist in 2 character states. (ex: present/absent)

Question 31

Convergent evolution

Answer 31

Convergent evolution describes the independent evolution of similar features in species of different lineages. Convergent evolution creates analogous structures that have similar form or function, but were not present in the last common ancestor of those groups. The cladistic term for the same phenomenon is homoplasy, (from Greek for same form). The recurrent evolution of flight is a classic example of convergent evolution. Flying insects, birds, and bats have all evolved the capacity of flight independently. They have “converged” on this useful trait.

Traits arising through convergent evolution are termed analogous structures, in contrast to homologous structures, which have a common origin, but not necessarily similar function. The anatomist Richard Owen was the first to recognize the fundamental difference between analogies and homologies. Bat and pterosaur wings are an example of analogous structures, while the bat wing is homologous to human and other mammal forearms, sharing an ancestral state despite serving different functions. The opposite of convergent evolution is divergent evolution, whereby related species evolve different traits. On a molecular level, this can happen due to random mutation unrelated to adaptive changes; see long branch attraction.

Convergent evolution is similar to, but distinguishable from, the phenomena of parallel evolution. Parallel evolution occurs when two independent but similar species evolve in the same direction and thus independently acquire similar characteristics—for instance gliding frogs have evolved in parallel from multiple types of tree frog.

Question 32

Can genealogical relationships among taxa be directly observed?

Answer 32

No

Question 33

Is the absence of a character a reliable dining character?

Answer 33

No

Question 34

Homologous

Answer 34

Homologous characters are found in 2 or more species and are derived from the same structure in a common ancestor.
Characters used for analysis must be homologous.