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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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    $\begingroup$ 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. $\endgroup$
    – Remi.b
    Commented Dec 8, 2013 at 10:19
  • $\begingroup$ @Remi.b Yes , but are CNVs genes ? Are there variation in no. of genes in population ? $\endgroup$
    – biogirl
    Commented Dec 8, 2013 at 15:15
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    $\begingroup$ 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) $\endgroup$
    – Remi.b
    Commented Dec 8, 2013 at 15:26
  • $\begingroup$ @Remi.b Hello! I think you have answered my question in the comments. Would you like to write an "answer" ? $\endgroup$
    – biogirl
    Commented Apr 29, 2014 at 15:40

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The position of a gene is not always fixed neither within nor between species. There are Copy Number Variation for example. 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 though. CNV, position of genes, regulatory sequences and other stuff are important too in the description and the functionality of a lineage.

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. For french speaker people this podcast(Follow: Biodiversité: Plus qu'une simple histoire de conservation/Pierre-Henry Gouyon) is of interest. You won't find the perfect objective definition of what is a species. Here and here are posts that discuss the definition of species.

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As Remi points out you are generally incorrect but the locality idea is specifically ok. The positions and types of mutations and divergence for specialization in certain genes regardless of their place in the genome is key in determining homology which is used for species determination at the molecular level. The drawback is: its rather expensive when most species differences are obvious at the phenotypic level.

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I would add:

Most categories in sciencie (species, order, living, planets, moons, stars, organs, fruits, etc.) are not "real". We (humans) create categories and attach objets to them in order to make general assumptions, so we can say things like "Most objects of category X have Y property."

Then, the way we define categories it's mainly the most practical way. And sometimes we addapt definitions, when there are practical motivations.

I think the motivation to define species related to the usual intra reproduction hability (and usual inter reproduction inhability) it's because that mantains certain homogeinity. Maybe a better definition would be something like "two groups of individuals belongs to the same specie if the rate of fertility among their individuals is > x %".

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