Phylogenies and Genome Evolution Flashcards
What is the out group?
Everything is compared to outgroup. Comparing everything against the same thing, can see how they are related
What can you see using a phylogenetic tree?
What organisms are related to another.
how proteins are related to another, or how proteins might be in the same family and have similar functions.
Can see where mutations occured. Phenotypic changes associated with mutations?
Ex: sequencing flu genome to see which vaccinations work and which dont, develop vaccines to work for this flu and related virusesCan see which genomes are affected by different things
Taxa
Come from common organism/ sequence
Sister taxa
Closer to each other than anything else on the tree
Monophyletic group
All descendants of a common ancestor and the common ancestor
Synthesis sequencing
Every time a base is incorporated it is detected
Generates a lot of genomic data quickly
Uses detection of byproducts of nucleotide incorporation into the chain to determine sequence
Pyro sequencing
Polymerase moves down a single base, many of same base are being added. Nucleotides added each round are of one base.
ATPs generated by pyrrophosphates being given off every time a base is added in. ATPs are convertd into light energy using an enzyme called luciferase. Light energy detected by the sequencing machine. When three bases incorporated at once, there is three times the amount of light energy so you get a triple peak.
Nucleotides (extra ones) need to be degraded so they dont get detected in the next round of replication. When wrong base, you dont get a peak becuase no pyrrophosphate is released to create light energy and ATP
Illumina sequencing
Library preparation- genome analyzer mass sequences a ton of fragments by using sound waves to break it up, incubate at temp with dATPs and taq will add As at end of blunt cut DNA.
size selection- run dna out on gel and your sample will make a smear, take secion of gel and you cut out a chunk at a certain size and you get a gel plug, you know the fragment length
cluster generation- dense lawn oligos that bind to the adapters ligated to the library fragments,the size selected single stranded DNA. DNA concentration is dilute so you dont end up with every single oligo bound to a fragment. Bridge amplification gives you clusters of same DNA sequences. Reverse strandds cleaved and washed away
sequencing- on geome analyzer genome clusters sequenced base by base using reversibly terminated flourescent nucleotides.
D-loop
No functional genes but accumulates mutations at a rapid rate, useful for ancestry studies
Mitochondrial lineages
Seven mitochondrial lineages probably gave rise to all that we have today, mutations accumulated that start new lineages, can look at dispersal patterns. Y chromosome is looked at as well to see parternal dispersion.
Phylogram
Shows amount of divergence by branch length, proportional to DNA changes
Comparative Genomics
Can predict time since divergence
- Molecular clock
- Most are random neutral mutations
- Sequence differences canbe used to estimate the time since divergence
- Higher rates of mutation may identify important regions that may be affected by selection
Molecular clock
Look for regions that are conserved within and between groups of organisms. Look at times of divergence based on sequences.
Want genes that accumulate mutations in specific intervals, evenly.
How do we estimate myr divergence?
Adaptive radiations: many fossils appearing all of a sudden the the fossil record with similar morphology.
Fossils can be carbon dated (half life of carbon) or other radioactive isotopes.
Look at ancestors of fossils, sequence genome and correlate number of differences in two genomes and number of mutations, predict when they diverged
Molecular based origins of diversity and evolution
Alternative splicing
Changes in gene number
Changes in regulatory sequences
Non-protein coding RNA regulation
Gene mutation
Our genome is relatively static besides few mutations, but over long expanses of time they can be dynamic.
Gene Comparisons
Differences in between organisms, some fixed differences- mutation that is in everyone in the population (allele frequency equals one). Found in one group of organisms so thought to be important, found in one group but not the other, sometimes people attribute important things to these mutations that arent valid.
Selective sweep
individuals that had these mutations are selected for very highly so the mutation would expand very quickly
FOXP2
- FOXP2 transcription factor known to function in human speech
- Human speech associatedwith two non-conservative aa changes (Asparagine 303 and Serine 325) occurred after humans and chimps diverged (6mya)
- Chimps and mice differ by only one nonconservative AA change (Asparagine 325) these two groups are at least 50my divergent
Transposable elements and diversity
Contribute more than anything to dynamic nature of genome. Over time there are increases in when a specific line is repeated in your genome.
Genome size has increased- Junk DNA can be attributed to transposable elements in a way becuase they replicate themselves over and over again(selfish, over represented number of copies)
How line transposable elements spread
Lines have original location, might be in non coding region, but have to have gene to create another DNA copy, and have to be able to integrate.
Codes for mRNA, gets transcibed and transported out of nucleus, translated
mRNA and proteins go back into the nucleus and we get cDNA being made (reverse transcriptase) integrase integrates DNA into genome. Lines recognize a small 4bp sequence as integration site, cuts chromosome open with endonuclease and inserts its genome, replicates itself within the genome. Now there are two copies
How do transposable elements work?
- Transposon can move from one area of the genome to another “Jump”
- Are not independent genetic elements (aren’t like plasmids)
- Have one gene that catalyzes transposition
- DNA is cut by transposase
- insertion sequence is inserted (by transposase)
- DNA polymerase and ligase fills it in
Are transposable elements good or bad?
Some copy and paste, some cut and paste, both jumping to different regions.
Only bad when they land in the middle of a gene or a promoter sequence. Gene probably wont be able to transcribe or translate.
Got most non coding DNA from transposable elements, its good becuase more likely the element will it non coding region of genome becuase there is more non coding DNA
Gene Duplication
Another way for an increase in number of DNA bases and maybe even a protein coding sequence that could be “modified” for an alternative function
This is how gene families arise. Were likely single gene with common ancestor but became many genes with related function.
What happens when you have two of the same gene?
Don’t need two copies of same gene, so when you duplicate that, it might be deleterious becuase you have 2x the amount(dosage effect). But second copy is free to vary, might stay the same, can accumulate mutations and it might be able to take on a different function, usually similar. Pseudo gene is a copy of the gene but it takes on so many mutations it becomes non functional
Unequal crossing over between duplicated genes
can increase the number of gene copies in the genome
Polymerase slippage can cause gene duplication, daughter strands are different combinations of original gene
Meiotic mishaps
Incorrect pairing of two homologues during meiosis
If mutation (duplicated gene) is inherited it will have two copies on one chromosome and one on the normal chromosome
Beta globin genes
Found on chromosome 11
