*p

*p becomes *h word-initially, which is usually subsequently lost.

*pá-(ta) ‘water’ → ā-tl (Huichol /háa/, Tübatulabal /paː-l/)
*páhi ‘three’ → ēi (Chemehuevi /pahi/)
*páka-(ta) ‘reed’ → āca-tl (Huichol /háka/, Tübatulabal /pahaːbɨ-l/ ‘sugar cane’)

*h may survive in cases where the following vowel is deleted, resulting in h before a consonant.

*píRwiR-(ta) ‘down’ → ihhui-tl ‘feather’ (O'odham vi:gĭ, Tübatulabal /piːwiː-l/)
*púnsa ‘wake up’ → ihza (O'odham vuha ‘wake up (trans.)’)

In some cases, h before a consonant may be deleted, with lengthening of the preceding vowel.

*púnsi-(ta) ‘eye’ → īx-tli (Huichol /hɨ́ʃi/, Tübulatulabal /punʒi-l/; compare *púnsa ‘wake up’ above)

Medial *p remains if the following vowel is stressed.

*hupáC-(ta)epa-tl ‘skunk’ (Huichol /ʔɨpá/ ‘skunk’, Mayo /huppa/ ‘skunk’, Hopi hovàa-ti ‘become smelly’)
*capóC-(ta)tzapo-tl ‘sweet fruit’ (Huichol /t͡sapú/)

Medial *p becomes h (which is subsequently lost) when the following vowel is unstressed.

*pípa-(ta) ‘tobacco’ → īye-tl (vowel length assumed; Hopi piiva)

In verbs, root-initial *p is treated as though it were medial, due to prefixes or proclitics.

*páta ‘melt, dissolve’ → pātla (Hopi paata; compare *pá-ta ‘water’ above)
*pakíC ‘enter’ → aqui (Hopi paki, pakìi-)

*t

*t generally remains t.

*tɨ́kɨ ‘cut’ → tequi (Hopi tuku)
*tɨ́n-(ta) ‘stone’ → te-tl (Tübatulabal /tɨn-t/, Hopi tùu- in tùupela ‘wall’, tùusö ‘rock shelter’)
*tɨ́RwiC ‘dust’ → teuh-tli (Tübatulabal /tɨːwi-t/ ‘dust’, Southern Paiute [tɨvip-pɨ] ‘earth’, Hopi tuuwa, -tuwa- ‘sand’)

*t becomes tl before *a.

*táka-(ta) ‘man’ → tlāca-tl (Hopi taaqa)
*tamV́n ‘tooth’ → tlan-tli (Huichol /taamé/, Tübatulabal /taman-t/, Hopi tama, tamàa-)

*k

*k remains k (= c, qu).

*ka ‘not’ → ca ‘not (irrealis)’ (Southern Paiute [qa])
*kalíR-(ta) ‘house’ → cal-li (Tübatulabal /haniː-l/, Southern Paiute [qani]ˢ)
*kápsi-(ta) ‘thigh’ → icxi-tl ‘leg, foot’ (Northern Tepehuan káji ‘leg’, Tübatulabal /hapʃi-l/ ‘thigh’, Hopi qàasi ‘thigh’)

*kʷ

*kʷ usually remains (= cu, uc).

*kʷasɨ́C ‘become cooked/ripe’ → iucci (Mayo /bʷasse/, Hopi kwasi, -kwasìi-)
*kʷayáC-(ta) ‘frog’ → cueya-tl (Northern Tepehuan babááda-i)
*kʷíka ‘sing’ → cuīca (Mayo-Yaqui /bʷiːka/)
*kʷitáC-(ta) ‘excrement’ → cuitla-tl (Huichol /kʷitá/)

becomes zero word-initially.

becomes h before a consonant (after deletion of the intervening vowel).

*suʔu-(ta) ‘grandmother’ → cih-tli (O'odham hu'u-l, Hopi so'o)
*suʔwiC-(ta) (?) ‘hare’ → cih-tli (Tübatulabal /ʃuːʔi-t/, Cupeño /suʔi-ʃ/, Hopi sowi, sowìi-)

*c

*c remains c (= tz) except before *i.

*canáC-(ta) ‘a kind of bird’ → tzana-tl ‘grackle’ (Cora /t͡saná/ ‘mockingbird’, O'odham ṣaṣañ ‘blackbird’, Yaqui /t͡ʃana/ ‘blackbird’)
*có-(ta) ‘snot’ → tzō-tl ‘filth’ (*có-co ‘boogers’ → Northern Tepehuan sóso-i, O'odham ṣoṣa; *co-... ‘boogers’ → Cora /t͡suʔumé/, Huichol /t͡sumé/)
*mɨ́ca-(ta) ‘moon’ → mētz-tli (Huichol /mɨ́t͡sa/, Tübatulabal /mɨːja-l/ ‘month’)
*ʔucúC-(ta) (?) ‘stinger’ → itz-tli ‘obsidian blade’ (O'odham 'u:ṣ ‘stinger; arrowhead’, Central Tarahumara /ut͡ʃú/ ‘sting’)

*c becomes ch before *i.

*cíCci-(ta) ‘saliva’ → chihchi-tl (Mayo /t͡ʃitt͡ʃi/)
*táCciC-(ta)tlach-tli ‘ballgame; ballcourt’ (Hopi tatsi, tatsìi- ‘shinny ball’)

*s

*s remains s (= z, c) except before *i.

*sɨ́p-(ta) ‘ice’ → ce-tl (Tübatulabal /sɨp-t/)
*sutɨ́n-(ta) ‘fingernail’ → izte-tl, izti-tl (Huichol /rɨté/, Tübatulabal /sulun-t/)

*s becomes [ʃ] (= x) before *i.

*síku-(ta) ‘navel’ → xīc-tli (Northern Tepehuan íkui, O'odham hig, Southern Paiute [siɣu]ⁿ)
*sísi-(ta) ‘excreta’ → xīx-tli (Huichol /ʃíʃi/ ‘urine’, O'odham hihi ‘intestines’)

*h

*h is lost.

*haki (?) ‘who’ → āc (Hopi hak, haki-)
*hupáC-(ta)epa-tl ‘skunk’ (Huichol /ʔɨpá/ ‘skunk’, Mayo /huppa/ ‘skunk’, Hopi hovàa-ti ‘become smelly’)

*m

*m remains m.

*má-(ta) ‘hand, arm’ → mā-tl ‘fathom’ (Tübatulabal /maː-l/)
*makáC ‘give’ → maca (Hopi maqa, maqàa-, Southern Paiute [maɣa-])
*mɨ́ca-(ta) ‘moon’ → mētz-tli (Huichol /mɨ́t͡sa/, Tübatulabal /mɨːja-l/)

*n

*n remains n.

*náwo ‘four’ → nāhui (Huichol /náu-ka/, Central Tarahumara nawó, Tübatulabal /naː-naːu/, Hopi naalö-yö-m)

*w

*w generally remains w (= hu, uh).

*wákɨ ‘become dry’ → huāqui (Northern Tepehuan gákɨ-i)
*wɨcɨ́C ‘fall’ → huetzi (Northern Tepehuan gɨɨ́kɨ-i)

*w before *o becomes *h, which is subsequently lost.

*wokón-(ta) ‘pine tree’ → oco-tl (Huichol /hukú/, Tübatulabal /wohomboː-l/)

*a

*a generally remains a.

In rare cases *a may become e.

*matáR-(ta) ‘grinding stone’ → metla-tl (Huichol /matá/, Hopi mata, matàa-, Southern Paiute [mara])
*nasíC-(ta) ‘ash’ → nex-tli (Huichol /naʃí/)

*i

*i remains i.

*e (from earlier ) assimilates to a before ma and pa.

*tɨ́ʔmatamal-li ‘tamale’ (Southern Paiute [tɨʔma] ‘roast under ashes’)

*o

*o remains o.

*u

...

misc.

*ahi monophthongizes to e.

*mahíC-(ta) ‘agave’ → me-tl (Huichol /mái/, Northern Tepehuan maí)
*tahíC-(ta) ‘fire’ → tle-tl (Huichol /tái/, Mayo /tahhi/)

Certain *VCV sequences monophthongize to ō.

*ʔáya-wɨt-(ta) ‘big turtle’ → āyō-tl ‘turtle’ (Huichol /ʔajé/ (?); *ʔáya-(ta) ‘turtle’ → Hopi aaya ‘rattle’, Southern Paiute /ʔaja/)
*...-wɨt-(ta) ‘big jaguar’ → ōcēlō-tl ‘jaguar’ (O'odham ʼo:ṣaḍ ‘jaguar’ is related but not cognate)
*cuwaka (?) ‘weep’ → chōca (Huichol /-t͡suaka/, Northern Tepehuan suaáka-i)
*siyo-ta (?) ‘produce flowers’ → xōtla ‘bloom’ (O'odham hiot)
*siyo-ci-(ta) (?) ‘little flower’ → xōchi-tl ‘flower’ (O'odham hiosi-g, Northern Tepehuan yooxí-ga-i)
*taCpun-ci-(mɨ) (?) ‘little rabbits’ → tōchi-n ‘rabbit’ (*taCpun-(ta) (?) ‘rabbit’ → Tübatulabal tahpun-t, Hopi taavo, tap-)
*nápo-ci-(ta) ‘little prickly pear cactus’ → nōch-tli ‘prickly pear’ (*napV ‘prickly pear cactus’ → Northern Tepehuan návo-i, Central Tarahumara napó, Hopi naavu)

The final vowel of noun roots is deleted if the preceding consonant is tz, ch, [s] (= z, c), x or l. (Roots involving other consonants may also delete the final vowel due to analogy with the possessed form.)

*mɨ́ca-(ta) ‘moon’ → mētz-tli
*ʔucúC-(ta) (?) ‘stinger’ → itz-tli ‘obsidian blade’
*nápo-ci-(ta) ‘little prickly pear cactus’ → nōch-tli ‘prickly pear’
*táCciC-(ta)tlach-tli ‘ballgame; ballcourt’
*nasíC-(ta) ‘ash’ → nex-tli
*púnsi-(ta) ‘eye’ → īx-tli
*sísi-(ta) ‘excreta’ → xīx-tli
*kalíR-(ta) ‘house’ → cal-li