… and what about
This presentation is the property of its rightful owner.
Sponsored Links
1 / 53

… and what about positive Darwinian selection? PowerPoint PPT Presentation


  • 67 Views
  • Uploaded on
  • Presentation posted in: General

… and what about positive Darwinian selection?. We have already discussed a test based on the ratio of fixed to polymorphic differences

Download Presentation

… and what about positive Darwinian selection?

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript


And what about positive darwinian selection

… and what about

positive Darwinian selection?


And what about positive darwinian selection

We have already discussed a test based on the ratio of fixed to polymorphic differences

We note that the McDonald-Kreitman test requires data from many individuals from two populations or species. Let’s assume we only have one sequence from each species.


And what about positive darwinian selection

The KA/KS test requires two aligned sequences only.


And what about positive darwinian selection

  • The assumptions of this method are:

  • all synonymous mutations are neutral, i.e., they do not affect the fitness of the organism,

  • (2) nonsynoymous mutations can be advantageous, neutral, or deleterious,

  • (3) nonsynonymous mutations that are advantageous will undergo fixation in a population much more rapidly than neutral mutations.

  • If advantageous selection plays a major role in the evolution of a protein, then the rate of nonsynonymous substitution should exceed the rate of synonymous substitution.


And what about positive darwinian selection

If positive selection predominates, then KA/KS > 1

If neutrality predominates, then KA/KS << 1


And what about positive darwinian selection

Prevalence of positive selection

3,595 groups of homologous sequences

In 17 gene groups, the ratio of nonsynonymous to synonymous substitution was significantly larger than 1.

Endo T, Ikeo K, Gojobori T. 1996. Large-scale search for genes on which positive selection may operate. Mol. Biol. Evol. 13:685-690.

~ 0.45%


And what about positive darwinian selection

Prevalence of positive selection

7,645 homologous gene groups from human, chimpanzee, and mouse.

In 6 groups, the ratio of nonsynonymous to synonymous substitution was significantly larger than 1, i.e., experienced positive Darwinian selection (Clark et al. 2003).

~ 0.08%


And what about positive darwinian selection

The vast majority of molecular evolution is neutral.

Change = Equivalence


And what about positive darwinian selection

  • Examples of extremeKA/KSvalues (>>1):

  • Glycophorin C = a red-cell membrane protein that serves as the receptor for a Plasmodium falciparum erythrocyte-binding protein, hence mediating one of P. falciparum’s invasion pathways in humans. Selective factor? Malaria.

  • Granulysin = a protein secreted by cytotoxic T cells when they attach to infected body cells. It creates holes in pathogens, such as Mycobacterium tuberculosi, and destroys them. Granulysin also induces apoptosis in infected cells. Selective factor? Tuberculosis.


And what about positive darwinian selection

Elevated KA/KS ratios are frequently found in sex-related genes, e.g., genes involved in mating behavior, fertilization, spermatogenesis, ejaculation, or sex determination.


And what about positive darwinian selection

Sperm lysin

Red: Nonsynonymous/Synonymous >> 1

Green: Nonsynonymous/Synonymous ~ 1

Gray: Nonsynonymous/Synonymous << 1


And what about positive darwinian selection

One of the highest KA/KS ratios (= 5.15) for a full-length protein was found in the 18-kilodalton protein in the acrosomal vesicle at the anterior of the sperm cell of several abalone species.


And what about positive darwinian selection

It is thought that sex-related genes are subject to positive selection for short periodsoftime during speciation as a means of erecting reproductive barriers that restrict gene flow between the speciating populations.


And what about positive darwinian selection

“A total of 585 of the 13,454 human-chimpanzee orthologs (4.4%) have observed KA/KS > 1.”

“Simulations show that estimates of KA/KS > 1 would be expected to occur simply by chance in at least 263 cases, if purifying selection is allowed to act non-uniformly across genes.”


And what about positive darwinian selection

Methodological caveats:

(1) The KA/KS test can only detect positive selection if the proportion of nonsynonymous substitutions that are adaptive is >70%.

(2) The KA/KS test can only detect positive selection if it occurred recently.

(3) The KA/KS test can only detect positive selection if there are few reversals (e.g., A to T to A).


And what about positive darwinian selection

In the KA/KS test we assumed that all synonymous changes are neutral.

It is possible, however, that not all synonymous changes are neutral.


And what about positive darwinian selection

For example, the fitness effects of synonymous and nonsynonymous mutations were experimentally shown to exhibit almost identical distributions in two protein-coding genes of Salmonella typhimurium (Lind et al. 2010).

In other words, a synonymous mutation was as likely to be deleterious as a nonsynonymous one.


And what about positive darwinian selection

What is the proportion of synonymous mutations by codon position?

First codon position = 6%

Second codon position = 0%

Third codon position = 69%

What is the proportion of neutral mutations by codon position?

First codon position = 21%

Second codon position= 7%

Third codon position = 42%


And what about positive darwinian selection

What is the proportion of synonymous mutations by codon position?

Second codon position = 0%

Third codon position = 69%

What is the proportion of neutral mutations by codon position?

Second codon position= 7%

Third codon position = 42%


And what about positive darwinian selection

What is the proportion of synonymous mutations by codon position?

Second codon position = 0%

Third codon position = 69%

What is the proportion of neutral mutations by codon position?

Second codon position= 7%

Third codon position = 42%

some nonsynonymous substitutions are completely neutral

Some synonymous substitutions are deleterious


And what about positive darwinian selection

Homoplasy = A structural resemblance that is due to parallelism or convergent evolution, rather than to common ancestry.


And what about positive darwinian selection

Are the horns homologous or homoplastic structures?


And what about positive darwinian selection

Hair Bone


And what about positive darwinian selection

Pisciformy

(fish shape)


And what about positive darwinian selection

Myrmecophagy

(ant-eating)


And what about positive darwinian selection

Active flight has evolved at least four times (in insects, pterosaurs, birds, and bats).

Bioaerial locomotion


And what about positive darwinian selection

Evolution of

lysozymes

in

ruminants,langurs

&

hoatzins


And what about positive darwinian selection

Foregut fermentersare not herbivores, they are bacteriovores!

Food for bacteria


And what about positive darwinian selection

Foregut fermentation has arisen independently at least three times in the evolution of placental mammals, at least once in marsupials, and at least once in birds.


And what about positive darwinian selection

Ruminants (e.g., cows, deer, sheep, giraffes)


And what about positive darwinian selection

Colobine monkeys (e.g., langurs)


And what about positive darwinian selection

Hoatzin (pronouced Watson), an enigmatic South American bird (most probably related to the cuckoos).


And what about positive darwinian selection

Convergent amino-acid replacements in lysozymes from the foregut of cow and langur. Only convergent replacements are shown, denoted by a one-letter abbreviation of the resultant amino acid followed by the position number at which the replacement occurred.


And what about positive darwinian selection

Adaptive replacements contribute to a better performance of lysozyme at low pH and confer protection against the proteolytic activities in the stomach.


And what about positive darwinian selection

Position 87


And what about positive darwinian selection

Position 87


  • Login