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Morphophonology (also morphophonemics, morphonology) is a branch of linguistics which studies:

• The phonological structure of morphemes.
• The combinatory phonic modifications of morphemes which happen when they are combined
• The alternative series which serve a morphological function.

Examples of a morphophonological alternatives in English include these distinctions:

• Plurals "-es" and "-s", as in "bus, buses", vs. "bun, buns".
• Plural of "-f" is "-ves", as in "leaf, leaves"
• Different pronunciations for the past tense marker "-ed".

English, being mostly an isolating language, does not have much morphophonology. Inflected and agglutinating languages may have extremely complicated systems, e.g. consonant gradation.

The English plural morpheme s is written the same regardless of its pronunciation: cats, dogs. This is a morphophonemic spelling. If English used a purely phonemic orthography, these would instead be spelled cats and dogz, because IPA: /s/ and /z/ are separate phonemes in English.

To some extent English orthography reflects the etymology of its words, and as such it is partially morphophonemic. This explains not only cats /s/ and dogs /z/, but also science /saɪ/ vs. unconscious /ʃ/, prejudice /prɛ/ vs. prequel /priː/, chased /t/ vs. loaded /ɪd/, sign /saɪn/ signature /sɪɡn/, nation /neɪ/ vs. nationalism /næ/, and special /spɛ/ vs. species /spiː/, etc.

Most morphophonemic orthographies, however, reflect only active morphology, like cats vs. dogs, or chased vs. loaded. Turkish and German both have broadly phonemic writing systems, but while German is morphophonemic, transcribing the "underlying" phonemes, Turkish is purely phonemic, transcribing surface phonemes only (at least traditionally; this appears to be changing). For example, Turkish has two words, /et/ 'meat' and /et/ 'to do', which in isolation appear to be homonyms. However, when a vowel follows, the roots diverge: /eti/ 'his meat', but /edir/ 'he does'. In Turkish when a root that ends in a /d/ appears without a following vowel, the /d/ becomes /t/, and that is reflected in the spelling: et, et, eti, edir.

German has a similar relationship between /t/ and /d/. The words for 'bath' and 'advice' are /bat/ and /rat/, but the verbal forms are /badən/ 'to bathe' and /ratən/ 'to advise'. However, they are spelled Bad, baden and Rat, raten as if the consonants didn't change at all. Indeed, a speaker may perceive that the final consonant in Bad is different from the final consonant of Rat because the inflections differ, even though they are pronounced the same. A morphophonemic orthography such as this has the advantage of maintaining the orthographic shape of the root regardless of the inflection, which aids in recognition while reading.

In the International Phonetic Alphabet, pipes (| |) are used to indicate a morphophonemic rather than phonemic representation.

Table. The underlying (morpho-phonemic), phonemic, and phonetic representations of four German and Turkish words. The forms in boldface are the ones chosen for the official orthographies. (In the Turkish examples, |Ü| represents an underlying high vowel that may surface as any one of the four phonemes /i y ɯ u/.)

	word	morpho- phonemic	phonemic	phonetic
German	Bad	|bad|	/bat/	[bat]
	baden	|badən|	/badən/	[badən]
	Rat	|rat|	/rat/	[ʀat]
	raten	|ratən|	/ratən/	[ʀatən]
Turkish	et	|ed|	/et/	[ɛt]
	edir	|edÜr|	/edir/	[edir]
	et	|et|	/et/	[ɛt]
	eti	|etÜ|	/eti/	[eti]

Another example of a morphophonemic orthography is modern Hangul, even more so the obsolete North Korean Chosŏn-ŏ sinch'ŏlchabŏp orthography.