What is phylogenomics?

Merging of genomics and evolutionary analysis/history

    What % of the human genome codes for proteins.

1.2%

 What is the C-value paradox?

The c-value is the total amount of DNA found in a cell. There is a lot of variation of the c-value in very different eukaryotes indicating that a huge portion of DNA is not functionally important.

*The amount of DNA does not necessarily correlate to complexity

* c-value = constancy factor

    Who discovered transposable elements and in what model system?

Barbara McClintock, while studying the inheritance of kernel color in corn.

   What % of the human genome is transposable elements?

44%

What is a potential cost of carrying so much non-coding DNA?

The time, energy, and resources required to replicate a genome burdened by parasitic DNA could place a limit on growth rates, particularly in small rapidly dividing organisms.

   Do bacteria and Archea have transposable elements?

Yes, on plasmids. Transposable elements on the main chromosome tend to be eliminated by selection or drift as a result of asexual reproduction.

    What is the difference between class 1 and class II transposable elements?

Class I elements are called retrotansposons and are the products of reverse transcription events (LINEs). They might have evolved from retroviruses. Retrosequences are also Class I elements. They amplify via RNA intermediates that are reverse transcribed and inserted in the genome (SINEs).

Class II elements are called transposons when they contain a coding sequence. They replicate via a DNA intermediate. Transposase catalyzes transposition.

    How could you consider transposable elements, “selfish genes” and at what level of selection would that imply evolution is acting on?.

They are parasites that transmit themselves at their host’s expense. Natural selection is acting at the level of genes within organisms.

   Where is it most likely that transposable elements will proliferate and why. 

 Heterochromatic regions near the centromere where few important coding sequences are because mutations in coding regions will likely be wiped out by purifying selection.

 Describe the genetic characteristics of the hybrid between the swamp and tammar wallaby and what happened to transposable elements in the hybrid as a result?

The DNA of the hybrid was virtually unmethylated. In many chromosomes, a retrotransposon KERV-1 exploded in copy number.

  What is a potential benefit of the presence of transposable elements and might explain their continued presence in the human genome?

The transposition of exons with LINEs resulted in exon shuffling. Transposition results in a novel gene. Functional portions of proteins can be recombined in novel ways.

*Also, could be neutral, or could cause potentially beneficial mutation.

   Where did the HMGCoA in Archaea come from, how, and how was this discovered?

? The HMGCoA gene in Archaea came from bacteria by lateral gene transfer (likely conjugation or transformation).This was discovered by constructing a phylogenetic tree for the gene and finding that it comes out in an anomalous location.

    What are the four mechanisms of gene transfer?

Transduction – when viral DNA in a host leave the host chromosome to propagate and take host DNA with it

Conjugation – copies of plasmids moving from one bacterial or archaeal cell to another

Transformation – taking up nucleic acids directly from the environment

Endosymbiosis – a cell from a different species begins living inside a host cell

  What’s the difference between transduction and transformation and is different than conjugation?

Transduction is when viral DNA takes up host DNA with it. Transformation is directly taking up nucleic acids from the environment.

   How could you determine if a gene originated from lateral gene transfer?

Scan the genome to see if any regions exhibit higher AT or CG pairs than usual for that organism. Or do the same with codons.

  Describe the evolution of organellar genomes, and that of rubisco in particular.  

Chloroplasts and mitochondria are remnants of bacteria taken up by endosymbiosis. Some genes are still in the organelle, some became nuclear DNA, and most were deleted. Rubisco is made of 2 parts one coming from nuclear DNA and the other coming from Chloroplast DNA. Gene transfers have occurred many times between organelle and nucleus.

    Why have some genes, but not all genes been transferred to the nuclear genome. 

More organelle specific functions make it better for those genes to be kept in the organelle.

 How important has LGT been for the evolution of eukaryotes?  How?

Very important, it gave eukaryotes new metabolic capabilities which allowed them to use existing resources more efficiently or to obtain new resources. It allowed ability of cellular respiration and photosynthesis.

    Describe some characteristics of parasite genomes?

Very small genomes, gain nucleotides and amino acids directly from hosts, contain virulence genes, vertebrate parasites often have many genes that code for variants of membrane proteins.

   On average, how different are homologous proteins in human and chimps?

2 amino acids different

1)    What is environmental sequencing and why is important/useful?

a.    Not all species can be cultivated in monocultures.

Sequencing genomes present in a particular environment. It’s useful for finding genetic info from organisms even if we don’t know about them.