2. Early Neolithic
Separate communities of genetically and linguistically distinct communities that domesticated plants and animals independently, but also in parallel with each other. Europe and the Near East also went through a similar situation.
Independent language phyla during the Early Neolithic in China (cf. Vovin, Robbeets, etc.):
Amuric = Nivkh
Koreanic
Old Liaodong = "Japanic" ("pre-Japonic" in the Liaodong and Korean Peninsulas)
Old Liaoxi = phylum that influenced Altaic via agricultural vocabulary, etc., but is not Altaic itself
Old Zhongyuan = "pre-Sinitic" ("isolate" substratum in Sinitic)
Old Shandong = "para-Austronesian"; very genetically and archaeologically distinct from Old Lower Yangtze; thus, likely a separate phylum unrelated to Old Lower Yangtze
Old Lower Yangtze (OLY) = "pre-Austronesian"
Old Middle Yangtze (OMY) = "pre-Hmong-Mien"
Old Lingnan = "pre-Austroasiatic"
Old Upper Yangtze = early Sino-Tibetan
Old Xiangxi = "pre-Tujia" ("isolate" substratum in Tujia)
Siangic
Migrations into China during the Bronze and Iron Ages (cf. Vovin, Robbeets, etc.):
Turkic
Mongolic
Tungusic
Yeniseian
Ruanruan
Indo-European (Tocharian)
(Note that I do not consider Altaic to be a true family, but rather a linguistic area, much like how the five language phyla of East Asia form a linguistic area.)
That's 18 phyla total during the Early Neolithic. There were likely even more.
Today, in China we have only 8 phyla:
Sino-Tibetan
Kra-Dai
Hmong-Mien
Austroasiatic
Turkic
Mongolic
Tungusic
Koreanic