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
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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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