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Allium virgunculae var. yakushimense
Family: AmaryllidaceaeJapanese: ヤクシマイトラッキョウ (Yakushima ito rakkyou)
This one had me 100% fooled: I have no idea what the difference is between this species and A. macrostemon. . . except maybe a little smaller, and the fact that it grows around mountain tops! (Maybe I'm not the only one: Apparently this wasn't recognized as a distinct variety until 1998! But then again, I don't know the difference between chives and leeks!) I spent a long time wondering what this plant was doing atop Hasa Dake until one day when we were eating pickled onions and a guide from whom I learned quite a bit mentioned this species that I had not yet heard of.
References:
Hotta, M. Taxonomical notes on plants in southern Japan IV. The Allium thunbergii group (Liliaceae) istributed in southern Kyushu and Ryukyu Islands Acta Phytotaxonomica et Geobotanica 49(1): 66. 1998
Tropicos.org. Missouri Botanical Garden. 17 Jun 2014
米倉浩司・梶田忠 (2003-) 「BG Plants 和名-学名インデックス」(YList),http://bean.bio.chiba-u.jp/bgplants/ylist_main.html(2014年6月18日).