batterham

Question 1

What was clarke trying to prove?

Answer 1

That selection was acting and maintaining polymorphisms

Question 2

Steps in Clarke Protocol

Answer 2

1. Genetic variation must be shown to exist (AdhF, AdhS)
2. Allele frequencies must be described over time in one population or through space across populations - explain polymorphism (stable cline - due to selection, AdhS more thermostable)
   WHAT IS SELECTIVE AGENT
3. Demonstrate phenotypic diversity among genotypes for an aspect of molecular function (different alcohol substrates) - temps rarely reached by files naturally
4. Postulate relevant, discriminatory selection agent - know enough of ecology, allele product differences
5. Differences in molecular function must be reflected in fitness differences in postulated selective regime (frequencies converge at intermediate frequency in absence of ethanol)
6. Natural populations reexamined
7. Test hypothesis by perturbing allele frequencies in natural population

Question 3

Clarkes experiment

Answer 3

Lack of noise in allele frequencies in face of potential for drift, pertubation experiments and parallel clines –>BALANCING SELECTION
but what is selective agent?!, type of balancing selection?!

Question 4

Clark approach

Answer 4

1. choose gene

2. find selective agent

Question 5

BETTER APPROACH TO CLARK

Answer 5

1. choose selective agent which has an impact on viability (heat stress, humidity)
2. Identify genes responsible for adaptation - mapping, candidate gene

Question 6

Bacteria chemostat experiments

Answer 6

T5 phage resistance used as marker.
Control nutrients. nutrient in - bacterial culture out. sample population through time - lacz1 and lacz2 allele over time
GROWTH RATE = FITNESS

Question 7

chemostat better

Answer 7

closed environment and with every volume of nutrient media added an equal volume of media, with bacteria in it, is removed, so volume is constant and population is continuously sampled

Selection is operating only at extremes when a novel selective pressure comes in e.g. lactose vs. artificial sugars

variation can be maintained not necessarily becuase of balancing selection, but because under a set of conditions all genotypes are equally fit

Question 8

body plan development - 3 possibilities

Answer 8

1. different gene sets in various species
2. same gene sets - differences in regulation in various species
3. same gene sets - differences in coding region in various species

Question 9

body plan question

Answer 9

Across the chordate taxon there is an immense body plan diversity. It has been found that the homeobox genes, that encode transcription factors which act to confer cell identity, are differentially expressed in different regions of different chordate species. Changes in body plan are consistent with changes in the patterns of gene expression of these homeobox genes. It has also been shown that reducing mRNA levels of these genes, one or two at a time, through RNAi, produces changes in body plan, that are predictable based on knowledge of the function of each Homeobox gene.
While this evidence does strongly suggest that different regulation patterns are conferring different body architectures, there is as of yet no mutation or difference in nucleotide sequence that can explain specifically what is causing these differences. Furthermore there is a debate as to what is meant by gene regulation. Given that Homeobox genes encode transcription factors that are themselves regulatory elements, a regulatory change could be in the cis-regulatory region or in the structural gene. Hence yes, the evidence is compelling, but it is not without its failings.