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Why exactly were bacteria and archaea kingdoms separated from the now unused kingdom of Monera? Aren't they the same? They are both prokaryotes, so what is the difference?

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I'm surprised this term shows up much anymore. Though it's a part of history now, the following paper by Woese demonstrated the three domain system long ago.

This, however, is the net result of the sequenced genomes of eukaryotes, archaea and bacteria:

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Source: Toward automatic reconstruction of a highly resolved tree of life.

The phylogenetic differences between these organisms shed light that bacteria and archaebacteria were not as closely related as was initially though, hence the abolishment of Monera.

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As you note, "Monera" includes both Bacteria and Archaea -- but genetic analysis and molecular comparisons reveal without a shadow of a doubt that Archaea share a more recent common ancestor with Eukaryota than they do with Bacteria. Consequently, "Monera" is a paraphyletic group, not a proper taxonomic category. Thus the term has been abandoned in favor of the three domain model.

Edit You'll find quite a nice explanation of this at the Wikipedia page for Monera. While modern evolutionary biology textbooks tend not to discuss the now outdated term "Monera", each of the following textbooks lays out the relation among the three domains and discusses the reasons that we avoid paraphyletic groups: Futuyma Evolution 2nd Edition, Herron and Freeman Evolutionary Analysis 5th edition, Bergstrom and Dugatkin Evolution 1st Edition, Zimmer and Emlen Evolution 1st edition, Barton et al Evolution 1st Edition. (Presumably other texts and other editions would cover the same ground).

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  • $\begingroup$ Can you substantiate with some references ? $\endgroup$ – Jayachandran Mar 3 '15 at 3:27
  • $\begingroup$ Any basic biology textbook will explain the relationship among Bacteria, Archaea, and Eukaryota. Any evolutionary biology textbook will describe the problems with paraphyletic groups. But you don't have to go that far afield. The second paragraph of the wikipedia entry on Monera lays out pretty much what I've written above: with links to explain the three kingdom system and the problem with paraphyletic groups: en.wikipedia.org/wiki/Monera $\endgroup$ – Corvus Mar 3 '15 at 5:03
  • $\begingroup$ If you know this much then please edit your answer and put appropriate references to it. Answers with out proper references are not welcomed even if you are 100% sure. $\endgroup$ – Jayachandran Mar 3 '15 at 7:13
  • $\begingroup$ A question: is the wikipedia an appropriate reference? The advantage is that it is so easy to access directly from here: no books to request, etc., etc. $\endgroup$ – Corvus Mar 3 '15 at 15:14
  • $\begingroup$ Wikipedia is an easily accessible free encyclopedia..OK.. you can use it as a reference or you can name the book you have referenced with the author's name. Am I clear ? $\endgroup$ – Jayachandran Mar 4 '15 at 3:31

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