'All except' is a slightly unnatural way of saying 'all but'. The subject of the relative clause is 'all', here having plural reference (back to 'species', also plural here), and it therefore governs the verb in the plural: thus 'are', not 'is'.
'One', on the other hand, is simply the object of the preposition 'but/except'. ('But' is more typically a conjunction, but functions prepositionally in this kind of construction).
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