Ch 2 - The tree of life

Question 2

Systematics

Answer 2

2 branches: taxonomy - Linnaeus, Genus species; Phylogenetics: how species are related (trees)

Question 3

How does tree structure aptly describe evolutionary history?

Answer 3

Dead branch - extinction; new branch - divergence; trunk - common ancestry; older branches - more ancient; end of branches - extant (existing) species

Question 4

Taxonomic categories, and name them

Answer 4

Levels of classification: Kingdom, Phyla, Class, Order, Family, Genus, Species (King Phillip cried out for good soup)

Question 5

Clade

Answer 5

aka monophyletic group, which includes all descendants of a common ancestor; a character state (ex. feathers) provides evidence - could be ancestral or derived

Question 6

Cladistics

Answer 6

Willi Hennig: phylogenetic systematics

Question 7

Divergence

Answer 7

New species formed and becoming more different

Question 8

Character

Answer 8

A trait, such as shape, size, also DNA sequences

Question 9

Character state

Answer 9

the version of a character: small/big, colour/none, etc.

Question 10

Species may share similar character state because…

Answer 10

Share ancestral state - symplesiomorphy; share a unique derived state - synapomorphy; by independent means (ie birds and bats have wings) - homoplasy (convergence (in distantly related)/parallelism (in closely related))

Question 11

Synapomorphy

Answer 11

Shared, derived characters - good indicator for closely related species or for a clade

Question 12

Symplesiomorphy

Answer 12

Share an ancestral state

Question 13

Autapomorphies

Answer 13

derived character states in only one lineage

Question 14

Homoplasy

Answer 14

Convergent evolution of independent origin, aka - not homology; also reversals may mask synapomorphies

Question 15

Convergent Evolution

Answer 15

independent origin of a trait in 2+ taxa

Question 16

Evolutionary reversal

Answer 16

Trait reverts back to ancestral type; this is homoplasy

Question 17

Polytomy

Answer 17

relationships without enough info to determine the branching order, clumped together as they stem from common ancestor

Question 18

Occam’s razor

Answer 18

“Simplest solution tends to be the best”. We want the fewest assumption and hypothetical things - law of succinctness

Question 19

Parsimony

Answer 19

Traits placed to minimize number of evolutionary steps, simplest explanation - shortest overall tree length - based on synapomorphies

Question 20

Basic progression to mammals

Answer 20

Tetrapod limbs, amnion, homeothermy (in mammals and birds)

Question 21

Paraphyletic

Answer 21

Some but not all descendants of a single common ancestor (ie reptiles did not all descends from the same common ancestor)

Question 22

Retrotransposons

Answer 22

Genomics approach: small section of selfreplicating DNA which inserts itself into genome - really rare, little chance of homoplasy

Question 23

Maximum likelihood

Answer 23

chooses model of evolutionary change (ie all nucleotides equally likely to change) - statistical: evaluates significance of tree shape; very time consuming, limits number of taxa you can examine

Question 24

Kimura method

Answer 24

parameter assumes the transitions are more likely than conversions

Question 25

Distance method

Answer 25

Don’t search all tree space; computes genetic distance among all pairs of taxa, smallest distance links pair (neighbour joining); compares how different they are (gives a value), reduces to node then recalculates matrix and repeat; fast, only makes one tree.

Question 26

The Molecular Clock

Answer 26

Genetic distances to measure evolutionary time; Dayhoff: compares proteins sequences; mostly linear; however, some proteins can evolve lots, others don’t (ie. conserved)

Question 27

Factors that affect mutation rate in different species

Answer 27

Lifespan (ie elephant vs bacteria), environment, accuracy of DNA polymerase

Question 28

Dayhoff method

Answer 28

Calculates score between changes in amino acids (ie Ile and Leu not too different, but Leu and Arg would have greater score)

Question 29

Calibrating molecular clock

Answer 29

If you have a known divergence time (fossil), then # changes/divergence time = x # substitutions/million years; also D = 2rt (D = proportion of changes, r = rate, t = time (Myr))

Question 30

Why are rapidly evolving DNA sequences only good for taxa that have diverged recently?

Answer 30

Doesn’t work for past ones since the changes would be too fast to determine branching

Question 31

Isthmus of Panama

Answer 31

Formed when North and South america, split the “gulf of mexico”, separated the sea urchin populations; good example of calibration

Question 32

Hybridization

Answer 32

Inbreeding b/w closely related species forming a “middle” one; creates a net in the tree (reticulated)

Question 33

Difficulties in phylogenic trees

Answer 33

Limited data (esp. extinct); DNA can change in several spots in concert; homoplasy; reversals hide relatedness; rapid evo. doesn’t allow enough time for lineages to develop unique character states; haplotype is fixed (lose 2nd one), ancestor on one side is polymorphic as well as the common ancestor