mtDNA control region/D-loop polymorphisms

John E. Stacy johnest at ulrik.uio.no
Mon Jan 4 09:54:57 EST 1993


Thanks to every one who shared their experiences and references 
regarding intraspecific length variation in the mitochondrial 
D-loop.  
 
In this posting I will list the references, letters I recieved 
and summarize some of the responses. 

References I recieved regarding D-loop structure, polymorphism 
and studies that exploit this polymorphism are:
*************************************************  
A.C. Wilson and co-workers: 
 
	PNAS 88:1597.  1991 
	Nature 350: 467.  1991. 
	Mol.Biol.Evol. 8:475.  1991. 

Wilkinson, G. S. and A. M. Chapman. 1991. Length and sequence variation 
in evening bat D-loop mtDNA. Genetics 128:607-617. 
[This study used PCR product lengths: the bat D-loop includes an 
81 bp seqeunce repeated between 5 and 8 times (have not found 
any mention of this in other taxa).]

Vigilant et al (Science 253(27 Sept 1991)1503-1507) 
[Comparing 610 nucleotides in 189 human individuals, they found 
substitutions at 179 sites and length changes at 22 sites. Searching 
the EMBL data base using Vigilant, the sequences used in the study are 
available.]
***************************************************

One response via e-mail reported low variation (Nancy Bowers, Penn. State). 
Her study animals are cichlid fishes from Lake Malawi, Africa. 
Bowers writes:

"There are very few fixed allelic differences at the isozyme level 
and we had hoped the D-loop region to provide some discrimanatory power.  
As it turns out, I am finding 0.3-1% intraspecific differences!
This is fairly low, even among fishes (intraspecific differences in a Lake
Tanganyika species is 5% and is 12% in an open ocean species like marlins).
...
"I am currently looking at population level variation and as expected, 
it to is very low."

Regarding PCR based methodology, Bowers writes:

"I have found the D-loop very easy to work
with and have used Tom Kocher's conserved primers for PCR."
		   ^^^^^^^^^^
>Tom Kocher's e-mail: T_Kocher at unhh.unh.edu

I seem to have lost Bowers, but here is her "normal" address:

Nancy Bowers
Intercollege Program in Ecology
Penn State Unviersity
University Park, PA  16802
**********************************************************************


In summary, at least two groups employ PCR based methodology. 
Regarding easily detectable length polymorhisms, Wilkinsin
and Chapman (see above) detect these using EtBr stained
agarose gels. The length polymorphism is due to a variable number 
of repeats of an 81 bp segment in the bat control region. I have 
seen no mention of a similar repeated segment in other animals.


Thanks again to every one who responded. 


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FROM: John E. Stacy           ||  "A cup of coffee in the morning
at the University of Oslo     ||   recapitulates phylogeny"
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