Comments by "Angry Kittens" (@AngryKittens) on "Kingdom of Majapahit - Wrath of the Khan - Extra History - # 2" video.
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Blame the mishmash of foreign influence for that, everything from Sanskrit, to Dutch, Arabic, Portuguese, etc. It was originally probably pronounced something like "Yawa", but centuries of colonial/foreign influence changed the language as well, such that the colonial pronunciation became the standard one. You can see another example of this in the modern Indonesian pronunciation of Yogyakarta (pronounced "dzhog-yakarta") versus the historical ancient Javanese pronunciation of "yog-yakarta".
V and J sounds are uncommon in Austronesian languages, and prior to colonial influence, loanwords from Sanskrit and Arabic containing them were pronounced closer to W/B and Y/D/Dy. Sanskrit deva(ta) (deity), for example, became Malay dewa and Filipino diwata.
Spellings are much more phonetic in the neighboring Philippines and in British-controlled areas in Borneo. Mostly because Spanish and English orthography is (mostly) identical to how we pronounce the Latin alphabet in English today.
Another example is the name of a type of war-boat in maritime Southeast Asia, pangajava, which is just one of the many very strange spellings in European colonial sources in Indonesia and Malaysia that became the "standard" spelling and became nativized. Other names include pangaio, penjajap, pangajaua, pangaia etc. It still retains its original pronunciation and much more accurate phonetic spelling in the Philippines: pangayaw (a prefixed word pang- + ayaw, literally "something used for war/sea raids"; i.e. a "raiding [ship]").
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