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Newsgroups: bionet.molbio.evolution
Subject: Re: (none)
Message-ID: <1990Sep24.225436.8108@nlm.nih.gov>
Date: 24 Sep 90 22:54:36 GMT
References: <9009241922.AA06292@genbank.bio.net>
Reply-To: states@artemis.NLM.NIH.GOV (David States)
Organization: National Library of Medicine, Bethesda, Md.
Lines: 66

In article <9009241922.AA06292@genbank.bio.net> MBY134@sysh.surrey.ac.uk writes:
>
>            SEQUENCE CONSERVATION WITHIN A SPECIES
>
>Does anybody have any refs/data/views on the amount of overall
>DNA sequence variation within species. A related question is
>the amount of sequence divergence found between closely
>related but distinct species. I am interested in how much
>sequence variation is tolerated within a species before
>species barriers intervene to restrict genetic exchange.

Polymorphisms occur in human genomic DNA at a rate of about one
in 600 bases.  Human immunodeficiency virus type I strains may differ
by as much as 20% (strain BRU vs. strain Z321) in overall sequence,
more in selected genes.

>The reason I am interested in this is that there is
>considerable pressure in bacterial taxonomy at the moment to
>classify any group of bacteria with greater than 70% DNA
>homology as belonging to the same species. I feel this would
>throw together many closely related but distinct species -
>including some I work with! The definition of a bacterial
>species is controversial since species barriers can not be
>empirically determined in prokaryotes. However, in sexual
>species I have vague recollections that the sequence variation
>found within species may be much less than this (true I
>believe for Homo sapiens); also - in well studied groups,
>pairs of closely related but distinct species may be found
>(eg. amongst primates, mice or drosophila?) that have very
>high levels of DNA homology.
>
>Does anyone have any data to support or refute my prejudices?

A number of issues need to be clarified.  The implication of sexual
fertility is that in general any pair of alleles between two individuals
can be exchanged and will retain function.  Even if sexual exchange
of genetic material can not be demonstrated in a given bacteria,
it is possible (although perhaps burdensome) that the equivalent
retention of functionality could be demonstrated using a gene
by gene approach with recombinant technology.  Demonstrating that
one or more genes failed to complement between individuals would
be equivalent to demonstrating that a mating would be sterile.

As for the 70% rule, is this supposed to refer to:

	the average over all genes?
	the average of all genes that have been sequenced?
	the minimum (or maximum) divergence of any pair of genes?
	an average over a defined set of genes?

Each of these would lead to a radically different set of conclusions.
Divergence rates differ greatly from gene to gene so an overall average
is problematic.  It might be possible to develop an empirical set
of relations based on a set of universal genes such as the tRNAs and
ribosomal RNAs, but I am not aware of this having been done.  In the
absence of an extensive study correlating sequence divergence and
genetic complementation, I would be loath to base speciation, which is
inherantly a functional qualifier, on an arbitrary numeric rule.

>Johnjoe McFadden
>Department of Microbiology,
>University of Surrey,

David States
National Center for Biotechnology Information
National Library of Medicine