As with many linguists working on Native American languages, Athabaskanists tend to use an Americanist phonetic notation system rather than IPA.
Since transcription practices in Americanist phonetic notation are not formally standardized, there are different symbols in use for the same sounds, a proliferation partly due to changes in typefaces and computing technology.
This convention is also found in all Athabaskan orthographies since true voiced stops and affricates are rare in the family, and unknown in the proto-language.
The asymmetric lack of retroflex fricatives in the Proto-Athabaskan inventory appears as a surprising gap, but Leer argued against them being distinguished from *š and *ž: "In my reconstruction, PA lacked distinctively reflexed *šʳ and *žʳ as opposed to plain *š and *ž".
The reconstruction of tone is an issue of major importance in Athabaskan language studies, as well as for the wider historical linguistics field.
He encountered tone in Tlingit in 1914 when working with Louis Shotridge, a student and consultant of Franz Boas, with whom Sapir described the minimal pair /qáːt/ "crippled" and /qaːt/ "sockeye salmon".
He then encountered tone in Tsuut'ina (Sarcee) and gradually became convinced that Proto-Athabaskan must be reconstructed as a tonal language, although he was concerned by apparently contradictory findings in Gwich'in, Deg Hit'an, and Navajo.
His student Fang-Kuei Li, whom Sapir described as "a very able Chinaman", had the benefit of speaking Mandarin Chinese and hence being well aware of tone.
Sapir and Fang-Kuei Li investigated tone in several other Athabaskan languages, including Mattole, Wailaki, Hupa, Dëne Sųłiné (Chipewyan), and Hare.
Both Li and Harry Hoijer both harbored suspicions that Proto-Athabaskan lacked tone entirely, but it took until 1964 when Michael Krauss published a paper in the International Journal of American Linguistics where he argued that Proto-Athabaskan instead had glottalization contrasts which developed independently into tones in the daughter languages or in some cases were lost.
The following table adapted from Rice & Hargus (2005:9) shows how the syllable codas of Proto-Athabaskan (PA) and the internal reconstruction of Pre-Proto-Athabaskan (PPA) correspond with those of the high-marked and low-marked languages.
Because obvious similarities in morphology are prevalent throughout all of the languages in the Athabaskan family, Proto-Athabaskan has an extensive reconstructed proto-morphology.
Hoijer's proposal is missing several elements which were described in detail later, but Kibrik's is not terribly different from Rice's.
A major distinction between the Kibrik and Rice versions is in the terminology, with Kibrik's "Standard Average Athabaskan" maintaining much of the traditional Athabaskanist terminology – still widely used – but Rice changing in favor of aspectual descriptions found in wider semantic and typological literature.
The terminology in comparison: Kari (1989) offers a rigorous foundation for the position class system that makes up the verb template in Athabaskan languages.
None of these alternatives has gained acceptance in the Athabaskan community, and Jeff Leer describes this situation: A better term would be something like "valentizers", since their principal function is to indicate the valence of the verb ...
Leer (2008:22) gives a newer, more complex reconstruction, which takes into account some rare correspondences with the Eyak yi- prefix.