Unit 1 - Chapter 25.2-4 Phylogenetic Systematics

Question 1

Phylogenetic Systematics

Answer 1

Also just called “systematics”.
The science of biodiversity and evolutionary relationships.
Includes taxonomy; and the discovery, description, and interpretation of diversity

Question 2

Cladogram

Answer 2

Phylogenetic tree… a branching chart that shows how species are related

Question 3

Clade

Answer 3

An ancestor and all of its descendants. Also called a “monophyletic group”

Question 4

Are evolutionary relationships known between different species?

Answer 4

Our proposed evolutionary relationships are all hypotheses.

Question 5

Steps of phylogenetic analysis

Answer 5

1. Select ingroup and outgroup taxa
2. Determine characters & character states
3. Determine character polarity
4. Analyze Character Matrix
5. Generate Cladograms
6. Use outgroup to define boundaries of clade

Question 6

Homology

Answer 6

Similarity in characters due to common ancestry

Question 7

Homoplasy

Answer 7

Similarity in characters NOT due to common ancestry, usually due to convergent evolution

Question 8

Character

Answer 8

An observable, inheritable trait of an organism. (number of limbs)

Question 9

Character state

Answer 9

The value or condition of a character in a specific species or organism. (four limbs)

Question 10

Character Polarity

Answer 10

Whether a character is ancestral or derived. this is RELATIVE

Question 11

Ancestral Character

Answer 11

A trait inherited from an ancestor that has since undergone little change.

Question 12

Derived Character

Answer 12

A trait that has been changed via evolution, the most recent trait. Ancestral character morphs into derived character via evolution

Question 13

Symplesiomorphy

Answer 13

A shared ancestral character. Something that is true about the clade, but also true about a broader clade

Question 14

Synapomorphy

Answer 14

Shared derived character. Something that is generally only true about the clade, barring convergent evolution.

Question 15

Character Matrix

Answer 15

Table where one axis is the organism and the other axis is the gene sequence or a series of characters

Question 16

Good traits of a genome for character matrix analysis

Answer 16

-Good if there are many copies of the genome
-If they mutate slowly, this is good at family/order/class level
-If quickly, good at genus/species/population level

Question 17

Nucleus (as a source of DNA in DNA analysis)

Answer 17

has dna from both parents, and a lot of dna, BUT there’s only one per cell.

Question 18

Mitochondria (in DNA analysis)

Answer 18

Has a circular genome, maternally inherited. 200-2500 kbp
Plenty per cell

Question 19

Chloroplasts (in DNA analysis)

Answer 19

Plenty per cell. 160 kbp

Question 20

kbp

Answer 20

kilo base pairs = 1000 base pairs

Question 21

rbcL

Answer 21

also called RuBisCO
protein found in all plants, binds to CO2. Most abundant protein on earth.

Question 22

PCR

Answer 22

Polymerase Chain Reaction: amplifying a target DNA sequence by replicating it (similar to DNA synthesis) in a lab

Question 23

NGS

Answer 23

Next Generation Sequencing: Computer programs sequencing billions of base pairs. a bit unwieldly, a LOT of information

Question 24

Paraphyletic Group

Answer 24

All organisms in the group share a common ancestor that’s in the group, BUT some descendants are excluded.

Question 25

Polyphyletic Group

Answer 25

Common ancestor of all organisms within the group is NOT included in the group.

Question 26

Common Ancestor Proximity vs Relation

Answer 26

Taxa with more recent common ancestor will be more closely related

Question 27

Phylogenetic Reconstruction based on Distance

Answer 27

Antiquated. Fuck it!

Question 28

Phylogenetic Reconstruction via Maximum Parsimony

Answer 28

Going through every possible cladogram and selecting the simplest

Question 29

Consensus Tree

Answer 29

Attempts to find the most probable tree from max parsimony analysis

Question 30

Strict Consensus tree

Answer 30

Only shows clades that are common among all cladogram designs: will not get specific if different trees argue different things

Question 31

Molecular Clock

Answer 31

Use of DNA sequence variation to estimate time of speciation. Based on assumption and not very accurate. E.G. of calibration: if Mitochondrial difference is 12% and speciation occurred 6MYA, then 2% change every MY THEN, you know that something 3MYA would be 6% different in mitochondrial DNA