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上代特殊仮名遣い【じょうだいとくしゅかなづかい】 is a Nara-period practice in which two distinct versions of certain syllables (called 甲類【こうるい】 and 乙類【おつるい】, and denoted by subscript 1 and 2 in Latin script) were consistently denoted using different manyogana. For example, the word we now write as 上【かみ】 is /kami1/, which could be rendered with the second syllable as 美, while 神【かみ】 is /kami2/, which could be rendered with the second syllable as 尾.

The Wikipedia article states that "the phonetic difference [between the two types] is unclear", so it looks like this isn't a solved problem. Even so, I would like to know what we do know about the phonetic differences between the 甲類 and 乙類 syllables (if we know anything at all).

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    That Wikipedia article is just screaming for a rewrite. This was one of the hottest issues in historical Japanese linguistics during the 20th century. Much research has been done and much is known (in as much as anything is ever known in dead languages). If anything, it is the non-linguistic camps (国学 and 国文学) that still claim things are unclear. The topic is too broad to cover here. I suggest that you read the standard references first and then come back with additional questions. See 1) Miyake (2003) and 2) Frellesvig (2011). For bonus, see Lange (1973).
    – Dono
    Apr 15 '14 at 0:36
  • @Dono Thanks for the references! I've started looking at them, and you're certainly right - there appears to be a lot more known than the Wikipedia article suggests. As such, I've voted to close this post as "too broad". I'll probably be back with more detailed questions once I've had time to digest the material.
    – senshin
    Apr 20 '14 at 0:17
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    @senshin, please add a link here to your new question if / when you post it. :) May 16 '14 at 22:02

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