BG1

Question 1

Chordate characteristics

Answer 1

1. notochord
   stiffening dorsal rod, pre dates spine
   made of cartilage.

Question 2

History of Phylogeny

Answer 2

Darwin 1850’s: tree of life, first phylogeny.
Haeckel (1870’s): hierachal tree of life, humans at the top.
20th cent: anglo american consensus phylogeny: Deuterosomes and Protosomes

Question 3

what are deuterosomes and protosomes

Answer 3

Deuterosomes: anus forms first in embyonic development (humans, tunicates.)
Protosomes: mouth forms first in embryonic development (molluscs, anneldis).

Question 4

why did traditional phylogenetics fail?

Answer 4

1. phyla are ancient and distantly related to each other.
2. objected methods were only developed in 1960s
3. lack of suitable characters.

Question 5

what were three traditional characters in phylogenetics`

Answer 5

1. cleavage
   division of cells in early embryo to produce blastomere cells which form the morula (compact mass)
2. blastopore fate
   blastula invaginates to create the gastrula = gastrulation (cavity formation)
3. coelom foramtion.
   principle body cavity: begins in gastrula stage

Question 6

what are the two main types of cleavage

Answer 6

spiral cleavage (protosome): blastomeres divide they shift relative to each oher, dividing assymetrically producing a spiral arrangement. 
Radial cleavage: (deuterosome): blasometes roughly equal size are produced in a symmetrical arrangement

Question 7

what are the two processes of coelom formation

Answer 7

1. schizocoely (protosomes): coelom forms by splitting mesodermal embryonic tissue into two layers.
2. enterocoely coelom forms from pouches pinched off of the digestive tract.

Question 8

Who is responsible for the origin of cladistics

Answer 8

1950 - will hennig

Question 9

what did will hennig argue

Answer 9

that we should

1. attend order of which taxa branch out, not just degree of divergence.
   - –> use cladograms to represent that order.
2. use shared derived (apomorphic) but not shared primitive (pleisomorphic) characters.
   - —> Taxa with many shared derived characters were likely to be related.

Question 10

what is the maximum parsiomony method

Answer 10

Method developed by hennig.
* assumes tree which requires fewest steps to explain data.
can be justified with probability.
* generally no longer used in phylogenetic reconstruction, as more explict methods used.

Question 11

what was the origin of DNA as a character of phylogenetic study

Answer 11

18S rDNA sequencing, bp position.

evolves slowly so used for phylum level phylogenetics

Question 12

what are the four main groups in the current tree of life

Answer 12

1. Basal taxa (protostoma no longer used)
2. Deuterostomia
3. Ecdysozoa: identified by molecular bio, all shed a cutiicle
4. Lophotrochozoa

Question 13

what is a phylogeny

Answer 13

a hypothesis with statistical uncertainty subject to falcification as new data accumulates.

Question 14

what is bootstrapping

Answer 14

a form of bayesian posterior probabilities.

calculates support or each node based on the random re-sampling of data and rebuilding of each tree.

Question 15

what is the rate of constancy assumption

Answer 15

most methods of tree construction assume different lineages accumulates character state changes at a constant rate.

Question 16

what happens if the rate constancy assumption is violated

Answer 16

algorthms will give inaccurate trees since rapidly evolving lineages will tend to be artifactually placed together.
The long branch problem

Question 17

give an example of the long branch problem

Answer 17

C. elegans have a high rate of molecular evoltuion so analysis classifed them with lophotrochozoa despite high evidence as ecdysozoa.

Question 18

what is long branch attraction

Answer 18

systematic error,
distantly related lineages which have a a similar molecular rate of change are incorrectly inferred ton be closely realted when they have more substituions in common with each other as they have more substitutions in total.`

Question 19

what is the relative rate test

Answer 19

tests whether different lineages are evolving at the same rate

Question 20

describe the relative rate test.

Answer 20

1. simple phylogeny ((A,B)C)
   K= no. o subs between species. count relative to outgroup.
2. if molecular clock is true than KAC = KBC.
3. if not true this implies unequal rates of molecular evolution in lineages.