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I know that species have been classified on basis of reproduction , DNA similarity , niche, etc.

Has there been a classification based on locus of genes ? What are the drawbacks/shortcomings of classifying this way ?

Isn't it simple to classify on this basis as - a species can have variation at a locus but the position of that locus with respect to a chromosome is fixed in every individual of that species. This fact can eliminate the subjective criteria of DNA similarity.

But I think this isn't valid for bacteria as there is so much recombination going on.

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The position of gene is not always fixed within a species. There are Copy Number Variant within species for examples. A great part of the variation within humans is due to CNV. I agree that it is important to consider other genetic variations than only the alleles. CNV, position of genes, regulatory sequences and other stuff are important too. The concept of species is a poor concept which is old as Aristotle and important in the christian culture but we have to accept that this concept is not a natural category. You won't find the perfect objective definition of what is a species. –  Remi.b Dec 8 '13 at 10:19
    
@Remi.b Yes , but are CNVs genes ? Are there variation in no. of genes in population ? –  biogirl Dec 8 '13 at 15:15
    
CNV's are DNA sequences of any length that are present at several different number of copies along individual in a population or along species. THese sequences can contain one or several genes. So the answer to your question is yes! There are variation in number of genes within a species. Here are two references that might interest you: adsabs.harvard.edu/abs/2006Natur.444..444R and genome.cshlp.org/content/16/8/949. You will as well find some information about CNV on the [wikipedia page] especially under "identification". (en.wikipedia.org/wiki/Copy-number_variation) –  Remi.b Dec 8 '13 at 15:26
    
@remi.b Alright.Thanks! –  biogirl Dec 8 '13 at 18:29
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