Sunday, 18 March 2012

Gorilla Gemone Sequence helping to understand Hominid speciation


Luba Varlakov (42897077) 

Kamilah(female) the western lowland gorilla(Gorilla gorilla gorilla) is the first gorilla to have its full genome sequenced. Gorillas are the last of the great apes (family Hominidae) to have their genome mapped.

Figure 1. Kamilah the gorilla

 

Gorillas share >96% of their genes with Humans and are our second closest relatives. Our closest relatives are Chimpanzees with a >98% similarity in the genome.

The gorilla sequence was used  in a five-way whole genome alignment(WGA) with the human, chimpanzee(Pan troglodytes), orang-utan(pongo abelii) and macaque (Macaca mulatta) genomes, concentrating on the Human(H)-Chimpanzee(C)-Gorilla(G) relationship.

The  WGA showed a 70% similarity between H, C and G gemones. Unexpectedly 15 % of the remaining 30% of G genome was shown to be more similar to the H genome than equivalent loci in the C genome, the reverse being true for the remaining 15%. This was attributed to incomplete lineage sorting(ILS) (genotype subsets exist within the population) in the ancestral H-C population. Precious research has shown such similarities between the Human and Orang-utan genomes due to ILS.
 
The ILS effects are not uniformly distributed though the genome, with the mean ILS in coding exons at 22%, the low percentages of ILS extending several hundred kbp from coding genes.The variation is attributed to the local differences between effective populations after H-C-G species divergence and prior H-C species divergence. >90% of the genome is within 300 kbp of a coding gene. Similar ILS effects are also observed in recent human evolution.   

The researchers concluded that Gorillas diverged from the Human-Chimpanzee common ancestor 8.5-12 million years ago.Chimpanzees from Humans 5.5-7 million years ago.  These findings indicate an earlier divergence then previously derived from molecular data but align better with fossil records.


The findings are based on the assumption that the rates of mutations are not constant. The researchers suggest that mutation rates should decrease with increase in body size and resulting increases in generation times. The model however also assumes that the population sizes are constant.


References:
Kerri Smith 2012 Gorilla joins the genome club Nature viewed 17/03/2012
 http://www.nature.com/news/gorilla-joins-the-genome-club-1.10185

Richard A Gibbs & Jeffrey Rogers 2012 Genomics: Gorilla gorilla gorilla Nature viewed 17/03/2012 http://www.nature.com/nature/journal/v483/n7388/full/483164a.html

Aylwyn Scally at el. 2012 Insights into hominid evolution from the gorilla genome sequence,  Nature. Vol:483  pp.169-175

Denis Venema  2011 Understanding Evolution: Speciation and Incomplete Lineage Sorting, viewed 18/03/2012  http://biologos.org/blog/understanding-evolution-speciation-and-incomplete-lineage-sorting

Asger Hobolth, Julien Y. Dutheil, John Hawks, et al., 2011 Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection, Genome Research. Vol: 21 pp.349-356











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