Subject: Re: [asa] historical versus experimental sciences

Just a quick note regarding mitochondrial DNA sequences not varying as much
as expected: sometimes that¹s because published ³mitochondrial² DNA
sequences (particularly from the non-coding control region) reported as
being mitochondrial are in fact copies (often multiple copies) that
transferred to the nucleus.

So in some cases the number of organism species is overestimated when
species ³identification² is based only on mitochondrial DNA sequences, and
the number of different DNA sequences is inflated because multiple
pseudogenes that coexist in one species are distinguished and assumed to
come from the mitochondria of different species.

In other cases, the number of distinct organism species can be
underestimated. For example, for technical reasons having to do with PCR
primer binding, sometimes one of the nuclear (pseudogene) copies of the
mitochondrial DNA sequences is preferentially detected in a group of related
species while the bona fide mitochondrial DNA sequences are not. Despite
probably having no function in the nucleus, relatively efficient DNA repair
mechanisms in the nucleus can conserve these DNA sequences more than in the
mitochondria, where relative lack of DNA repair mechanisms and relative
abundance of DNA-damaging free radicals can cause pretty rapid evolutionary
change. So, people compare what they think are mitochondrial DNA sequences
and find surprisingly little variation, leading them to classify the
organisms as a single species with some intraspecific population-level
variation. Had they really sequenced mitochondrial DNA, they would have
seen more differences between the organisms, which in fact belong to
separate species.

Here are a few examples:

Mitochondrial pseudogenes in the nuclear genome of Aedes aegypti mosquitoes:
implications for past and future population genetic studies.
> Hlaing T, Tun-Lin W, Somboon P, Socheat D, Setha T, Min S, Chang MS, Walton C.
> BMC Genet. 2009 Mar 6;10:11.
>
False phylogenies on wood mice due to cryptic cytochrome-b pseudogene.
> Dubey S, Michaux J, Brünner H, Hutterer R, Vogel P.
> Mol Phylogenet Evol. 2009 Mar;50(3):633-41. Epub 2008 Dec 24.
>
Many species in one: DNA barcoding overestimates the number of species when
nuclear mitochondrial pseudogenes are coamplified.
> Song H, Buhay JE, Whiting MF, Crandall KA.
> Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13486-91. Epub 2008 Aug 29.
>

To unsubscribe, send a message to majordomo@calvin.edu with
"unsubscribe asa" (no quotes) as the body of the message.
Received on Fri Aug 21 11:38:36 2009