Assignment for Friday:
Assignments for Monday
- Read through the Wikipedia entries fro UPGMA and Neighbor Joining
- Read Walter Fitch's article on types of homology (available on HuskyCT or here)
Assignment for today: Read excerpts of Chapters 5 and 6 from Li's "Molecular Evolution"
Introns and Their EvolutionThree groups of introns based on their splicing mechanisms:group I and II are self-splicing [have different splicing mechanism: see this figure for comparison of splicing]:group III introns are present in eukaryotic nucleus, need spliceosomes to splice out: Where different groups of introns occur?
Where do spliceosomal introns come from and how the splicing machinery evolved?Hypothesis:Spliceosomal introns evolved from Class II introns; the function of some of the internal loops of the class II introns are taken over by the spliceosomal snRNA (small nuclear RNA).Support:
Gratuitous complexity hypothesis for evolution of spliceosomal machinery: See reading assignment on WebCT [the portions for the reading are highlighted in the PDF file] Problem:class II introns are found in bacteria, and only in one Archaeal genus, Methanosarcina; why is it that predominately "crown-group" eukaryotes have introns?Not much of a splice site consensus (exon1 GT-intron-AT exon2, see here for the splice site consensus in Arabidopsis) Group I introns often have homing endonucleases. Also: reverse splicing Possible benefits of having introns:Exon shuffling, alternative splicing (1 gene -> different protein products) ....Two rival hypotheses: Intron Early vs. Intron LateIntron early:Protein diversity arose in analogy to exon shuffling in the generation of antibody diversity (see your biochemistry or genetics textbook on the maturation of the immune system).Claims:
Intron late:Present day introns are late invaders of already functional genes. Exon shuffling might play some role in eukaryotes, but most of protein diversity arose before introns invaded protein coding genes.Claims:
Compromise:mixed model of intron evolution
Else:it was suggested that class II introns were the reason for the separation between transcription and translation in Eukaryotes (accomplished through the nuclear envelope). Martin and Koonin's hypothesis suggests that class 2 introns were brought into the eukaryotic cell by the mitochondrial endosymbiont.
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Discussion - two debate teams on the function of introns in evolution:
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Goals class 16:
PRO INTRONS EARLY:
PRO INTRONS LATE :
From:<http://dml.cmnh.org/2002Jul/msg00351.html> ----- Original Message ----- > > --+--+-----------A This _is_ a Hennigian comb, because in a cladogram, _only_ topology counts. --+--F ... what a side branch is lies completely in the hand of the presentator.
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sequence space slides
Intro to phylogenetic reconstruction
Phylogenetic analysis is an inference of evolutionary relationships between organisms.
Those relationships are usually represented by tree-like diagrams.
Note: the assumption of exclusively tree-likeliness of evolution is not justified.Steps of the phylogenetic analysis:
Compilation of sequence dataset
Alignment
Determination of substitution model
Tree building
Tree evaluation
Why phylogenetic reconstruction of molecular evolution? A) Systematic classification of organisms e.g.:
Who were the first angiosperms? (i.e. where are the first angiosperms located
relative Where in the tree of life is the last common ancestor located? B) Evolution of molecules e.g.: domain shuffling, reassignment of function, gene duplications, horizontal gene transfer, drug targets, detection of genes that drive evolution of a species/population (e.g. influenca virus, see here for more examples) C) Identification of organisms
How: 1) Obtain sequencesSequencing Databank Searches -> ncbi a) entrez, b) BLAST, c) blast of pre-release data Friends
2) Determine homology (see notes for earlier classes for practical implementation)Reminder on Definitions: 3) Align sequences
4) Reconstruct evolutionary history
(e.g.: smallest error between distance matrix and distances in tree), or use ii) algorithmic approaches (UPGMA or neighbor joining)
find that tree that explains sequence data with minimum number of substitutions (tree includes hypothesis of sequence at each of the nodes)
given a model for sequence evolution, find the tree that has the highest probability under this model. This approach can also be used to successively refine the model. Bayesian statistics use ML analyses to calculate posterior probabilities for trees, clades and evolutionary parameters. Especially MCMC approaches have become very popular in the last year, because they allow to estimate evolutionary parameters (e.g., which site in a virus protein is under positive selection), without assuming that one actually knows the "true" phylogeny.
D
- ...) Else:
5) Interpret the result.
6) Discussion: How can a tree be rooted? |