Crosslinguistically rare sounds may be uncommon as a result of being phonologically marked (Trubetzkoy 1939) or due to articulatory or perceptual biases (Maddieson 1998). Certain types of sound changes are often argued to have roots in articulatory and perceptual biases (Blevins 2004). But in cases where there is limited data available, such as with understudied languages, it may be difficult to find evidence for the roots of sound changes. Synchronic variation can be used to provide evidence for diachronic sound changes (Blevins 2004; Lindblom 1990; Ohala 1993), which is particularly useful when historical data is limited. In this investigation we discuss phonetic biases, including acoustic and perceptual factors, that contribute to a set of sound changes in Tlingit, a critically endangered Indigenous language of Alaska, British Columbia, and the Yukon, that resulted in a primary split-merger (Blust 2012). This investigation provides further support for including explicit discussion of synchronic variation as part of the description of understudied languages. We propose that there should be a stronger emphasis on documenting and analyzing variation within understudied languages because excluding variation potentially masks significant intralinguistic and crosslinguistic phenomena.