Phylogenomics and Genotypic Adaptations

1
Phylogenomics and Genotypic Adaptations
2

• The C-value paradox
• In eukaryotes
• C-value total DNA in a cell
• No relationship between C-value and phylogenetic
  position on tree of life.
• Amoeba dubia 670 billion kb of DNA
• Drosophila melanogaster 180,000 kb of DNA
• Homo sapiens 3.4 billion kb of DNA
• c. 1.2 codes for proteins
• Human DNA is dominated by parasitic DNA
  (sequences that are not transcribed into products)

3

• Transposable Genetic Elements
• DNA sequence (information) that can copy and move
  a copy of itself to a new location
• Widespread (bacteria, archaea, and eukaryotes)
• Diverse and abundant
• Most are genomic parasites
• Time and energy spent in their replication at the
  expense of a host genome.
• Over 44 of human DNA is derived from
  transposable elements.

4

• Different classes of elements
• Different families in classes
• Most TGE leave a copy in place when the
  replicated copy is translocated
• If TGEs differ in replication capacity, natural
  selection can occur at level of pieces of DNA.
• Fitness of a TGE related to increasing its
  number.
• Spread of TGEs is faster in sexually reproducing
  organisms. Recombination provides more
  transposition sites.
• Negative effects of parasitic DNA
• 1. Replication of host DNA also means replication
  of extraordinary numbers of TGEs.
• 2. If TGEs move into coding sequences (exons),
  the function of this gene is typically knocked
  out.

5
Selfish genes and Levels of Selection

• NS can act at gene level if
• 1. the fitness of a particular sequence is
  independent of the fate of other sequences in the
  same genome.
• 2. there is variable success in spreading.
• Countering the spread of TGEs
• Purifying selection (automatic) death of a cell
  eliminates TGSs that have caused its demise.
• Evidence of purifying selection TGEs should be
  concentrated in DNA that is not expressed.
• E.g., heterochromatin e.g., near the centromere

6
Cellular Defenses

• Eukaryotes carry melthylases (add methyl groups
  to certain bases.
• 1. Prevents genes from being expressed
• 2. Prevents population growth of TGEs.
• Wallaby hybrid lacks methylation.

Single-stranded TGE DNA labeled with fluorescent
marker Hybridized to the TGE DNA in hybrid
wallaby chromosomes Reveals exposive growth of
the TGE population
No DNA hybridization occurred in progenitor
species
7
Benefits derived from transposable elements

• 1. Exon shuffling (produces novel genes)

8
Benefits derived from transposable elements

• A key event in evolution of the eukaryotic immune
  system
• adding a key gene from a transposable element.

Somatic recombination
9

• RAG1 and RAG2 can also catalyze transposition of
  gene constructs.
• Identical to transposition by transposable
  elements

RAG1 RAG2 transposases Can mediate
transposition independent of location
10

• Evolutionary hypothesis
• Two insertions of a transposable element into a
  membrane protein gene
• Early in vertebrate evolution (several hundred
  million years ago)
• Element duplications

Two transpositions into a membrane protein
gene Subdivision into initial V, D, J segments
11

• Lateral gene transfer (eukaryotes)
• 1. Endosymbiosis a cell from a different
  species begins living inside a host cell.
• e.g., bacteria associated with ancestors of
  present day eukaryotic cells ? mitochondria and
  chloroplasts
• Bacteria have c. 5,000 genes, therefore,
  acquisition of mitochondria and chloroplastids
  represents the largest lateral transfer events in
  the history of life.

Phylogenetic position
12

• Other resemblances of mitochondria and
  chloroplasts to bacteria
• 1. Size
• 2. Bacteria-like circular chromosome
• The double membrane

13

• Plastids
• 2. Lateral transfer of genes via secondary
  endosymbiosis
• A eukaryotic cell with a chloroplast is
  incorporated into a eukaryotic cell that lacks
  one.
• Retention of the chloroplast represents
  acquisition by secondary endosymbiosis.

The evidence
14

• Cryptomonas F a green alga
• Chloroplastid is enclosed in four membranes
• A typical circular DNA is located inside the
  inner membrane pair
• Between the inner and outer pairs of membrane is
  a nucleomorph.
• The nucleomorph codes for a functional ribosome
  that remains between the two pairs of membranes.
• Because the rRNAs of nucleomorph and nucleus are
  very different,
• Conclusion The outer pair of chloroplastid
  membranes and the nucleomorph are vestiges of the
  original host cell.