Question

1)Based on the Flynn et al paper, how do topologies generated by parsimony methods compare with those from model based analyses?

2)Explain neutral theory, briefly. Why does the molecular clock depend on neutral theory?

3)What is a gene tree and how is it different from a species tree?

4)In your own words, what is long branch attraction?

Answer 1

Aus Neutral theory : evo- The neutral theory of molecular evolution holds that most lutionary changes at the molecular level, and most of the variation within and between species, are due to random genetic drift of mutants alleles that are selectively neutral. So, according to neutral theory, when we see several versions of gene in a population, it is likely that their frequencies are simply drifting around. The data supporting and refusing the neutral theory are complicated. H an er Most importantly, the neutral theory is not an alternative to theory of evolution, it is simply an elaboration of a small part of evolutionary theory. Relationship with neutral theory: and the observation of a clock-like rate of molecular change was originally purely phenomenological. Later, Motoo Kimura developed neutral theory the of molecular evalution, which predicted a molecular clock. S If most changes seen during molecular evolution are neutral, then finations in a population will accumulate at a clocka rate that is equal to the rate of neutral mutations in an india vidual That is why molecular clock depends on neutral theory.

3. Gene Tree: ® Gene trees represent the evolutionary history of the genes inches- ded in the study. Gene trees can provide evidence for gene duplication events, as well as speciation events. illalla Sequences from different homologs can be included in a gene tree, the subsequent analyses should cluster osthologs, thes demonstrating the evolutionary history of the othologs. But, species trees should contain sequences from oney orthologay genes. Son proust o n Like this, gene tree is different from species tree. 4. Long branch attraction! Incorrectly clustering of outlier organisms due to shared dissimilarity to the main group. Long branch attraction means that outgroup organisms are not clustered due to similarity among them, they are clustered due to shared dissimilarity to the main group of organisms. Long branch ranch attraction is I attraction is a a systematic error su in clustering of sequences and does not show true evolutionary relationships. long branch attraction also known as "LBAY