I know many words for animals are usually written in katakana in contemporary Japanese, even though kanji exist:
- イルカ
- クマ
And it seems some very common domestic animals I don't seem to notice written in katakana:
- 猫{ねこ}
- 犬{いぬ}
Then there's some others I'm not sure about but have a hunch, including organisms that are not "animals":
- クモ spider
- ケヤキ zelkova (a kind of tree)
- 魚 fish
- 鳥 bird
- 馬 horse
- 牛 cow
Are there some patterns or rules of thumb I should learn? Wiktionary doesn't seem reliable enough to look up which variant to prefer, which other free resource is better, especially when my Japanese isn't good enough to use monolingual sources?
Is it something to do with very common terms being exceptions? Or domesticated vs undomesticated? Or general terms vs more specific terms closer to individual species? Are the rules the same for animals, insects, birds, fish, and plants?
Answer
If the kanji for that word is not part of the list of joyo kanji, you should probably go for the kana equivalent. The word is already sort of done for you in this sense. The ones that you're already familiar with, like 魚, 鳥, 馬, 牛, etc. are all common, and you were able to come up with them pretty easily. Something like 欅 though... could you read that? No? Neither can a lot of native speakers, and that is connected to it not being included in the joyo kanji.
There are kanji for most of these things, and native speakers might know a few of them, but in general they are the territory for people who like to go above and beyond. These are the kinds of things you'll find on the upper levels of the 漢字検定, almost at a level of trivia knowledge.
If a kanji is joyo, then theoretically everyone should be able to read it. If it's not, then there's no guarantee, and as the kanji itself gets more obscure the more likely it is to be kana only. For a hard rule, though, joyo is going to be where you go.
That said, however, it is possible to take kanji that do appear on the joyo list and write them in kana anyway. An example in your post is クマ. Sometimes you might see this written in kana, even though its kanji, 熊, is on the joyo list and common enough to be widely known. But when it appears in compounds, like in アライグマ, it will not be written in kanji.
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