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Inspired by this recent question on Greenberg's classification of African languages, I wonder about the current state of classification of the American languages. (By "American" I mean the indigenous pre-Columbian languages and their descendants).

Greenberg controversially proposed just three macrofamilies of American languages (Eskimo-Aleut, Na-Dené, and the "everything else" family Amerind) but this seems to have been some significantly flawed research. The 1964 "Consensus" Classification classified 16 phyla; and Campbell and Mithun's 1979 "Black Book" took a conservative approach resulting in dozens of likely families and many isolates.

I'm asking for a summary of the current state of research in this area. I'm not trying to start a lumper vs. splitter discussion, nor am I looking for popular-press summaries but for a sense of what's currently going on in scholarly work.

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    Campbell 1997 is the consensus source, I think. It's certainly the place to start and covers everything on the topic up until then exhaustively. There really haven't been major shifts since then that I've been aware of; but I'm not a specialist. – jlawler Aug 31 '12 at 0:49
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    Thanks @jlawler, turns out our library has a copy and I've requested it. – Mark Beadles Aug 31 '12 at 1:32
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    Something that seems settled now, too, is that the last two waves of migration (Eskimo-Aleut and Eyak-Athabascan) have extra-N.American relatives. Eskimo-Aleut languages are spoken from Siberia to Greenland, and Ed Vajda seems to have established a relation recently between some Yeniseian languages in Siberia and Eyak-Athabascan. The other languages in N/S.America appear to have arrived earlier than those two language groups. – jlawler Aug 31 '12 at 19:26
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    The book just arrived in the campus mail - I'll give a summary if it looks like it helps answer my question. – Mark Beadles Sep 10 '12 at 20:13
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    @jlawler As to Ed Vajda's proposal, it has been challenged by Stefan Georg and George Starostin, both reputable experts on Ket and other Yeniseian languages, who have criticized (independently of each other) Vajda's interpretation of the morphological data, especially of what Vajda considers vestigial markers supposedly inherited from the hypothetical Proto-Dene-Yeniseian. See also the highly critical review by Lyle Campbell: Review of The Dene-Yeniseian Connection (2011). – Pavel Jetušek Aug 14 '15 at 18:17
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I think you can find a fairly reliable (more reliable than the Ethnologue, I would say) and pretty much consensual (meaning that even long-rangers would not object to it other than go much further in their speculations, hypothesizing deeper links between them) information in the Glottolog catalogue, as its authors generally tend to avoid controversial classifications that have not gained wider acceptance yet. It does not mean that at least some of the families and isolates are not related, but their relationship may be too deep to ever discover, or the research carried out so far has not met methodological standards, or, perhaps, no particular research into their relationship has been carried out yet.

Anyway, if you restrict the listing found on that Glottolog page to the North America and South America macroareas, you will get a list of top-level families and isolates including those that are not indigenous to the New World. Leaving the relative newcomers, pidgins, mixed languages, sign languages, unattested languages, unclassifiable languages and artificial languages out, you will get a list similar to the following:

  • NORTH AMERICA / Top-level families:

    • Algic, Athabaskan-Eyak-Tlingit, Caddoan, Chimakuan, Chinookan, Chumashan, Cochimi-Yuman, Coosan, Eskimo-Aleut, Haida, Huavean, Iroquoian, Jicaquean, Kalapuyan, Keresan, Kiowa-Tanoan, Lencan, Maiduan, Mayan, Misumalpan, Miwok-Costanoan, Mixe-Zoque, Muskogean, Otomanguean, Palaihnihan, Pomoan, Sahaptian, Salishan, Shastan, Siouan, Tarascan, Tequistlatecan, Totonacan, Tsimshian, Uto-Aztecan, Wakashan, Wintuan, Xincan, Yokutsan, Yuki-Wappo
  • NORTH AMERICA / Isolates:

    • Adai, Alsea, Atakapa, Beothuk, Cayuse, Coahuilteco, Comecrudo, Cotoname, Cuitlatec, Esselen, Guaicurian, Chimariko, Chitimacha, Karankawa, Karok, Klamath-Modoc, Kutenai, Maratino, Molale, Natchez, Salinan, Seri, Siuslaw, Takelma, Timucua, Tonkawa, Tunica, Washo, Yana, Yuchi, Zuni
  • BOTH NORTH & SOUTH / Top-level families:

    • Arawakan, Chibchan
  • SOUTH AMERICA / Top-level families:

    • Araucanian, Arawan, Aymara, Barbacoan, Boran, Bororoan, Cahuapanan, Cariban, Chapacuran, Charruan, Chocoan, Chonan, Guahibo, Guaicuruan, Harakmbut, Hibito-Cholon, Huarpean, Huitotoan, Jivaroan, Kakua-Nukak, Kamakanan, Kariri, Katukinan, Kawesqar, Lengua-Mascoy, Matacoan, Nadahup, Nambiquaran, Nuclear-Macro-Je, Panoan, Peba-Yagua, Pri, Quechuan, Saliban, Tacanan, Ticuna-Yuri, Tucanoan, Tupian, Uru-Chipaya, Yanomam, Zamucoan, Zaparoan
  • SOUTH AMERICA / Isolates:

    • Aewa, Aikanã, Andaqui, Andoque, Arutani, Atacame, Betoi, Camsá, Candoshi-Shapra, Canichana, Cayubaba, Chiquitano, Chono, Cofán, Culli, Fulniô, Guachi, Guamo, Guató, Irántxe, Itonama, Jirajaran, Kanoê, Kunza, Kwaza, Leco, Lule, Máku, Matanawi, Mato Grosso Arára, Mochica, Mosetén-Chimané, Movima, Muniche, Mure, Omurano, Oti, Otomaco, Páez, Pankararú, Payagua, Pirahã, Puelche, Puinave, Pumé, Puquina, Ramanos, Sapé, Sechuran, Tallán, Taruma, Taushiro, Timote-Cuica, Tinigua, Trumai, Tuxá, Urarian, Vilela, Waorani, Warao, Xukurú, Yámana, Yuracaré, Yurumangui, Yuwana

One of the great features of Glottolog is that it also collects all the relevant bibliographical references, so any research you would like to carry out yourself may well start right there. Check out the Haida listing, for example, where you can see the internal classification, useful comments and, of course, a long list of useful references.

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