Allophone

An allophone is a conditioned realisation of the same phoneme. Allophones can be complementary allophones which are distributed throughout speech predictably and with regards to the phonetic environment. Allophones can also be free variants.

Whether something is an allophone or a phoneme within a language can affect the phonological perceptual boundary. Kazanina et al. (2006) did a study on Russian and Korean speakers' perception of [t] and [d]. In Russian there is phonemic contrast beween [t] and [d] and in Korean they are allophones of the same phoneme. The study found that there was a mismatch field (MMF) in a MEG scan when the subjects were presented with each token. In the Korean speaker no mismatch field was present, however in the Russian speakers there was.

Example:
If an English word has a [p] in initial position followed by a vowel then it will be realised with aspiration [pʰ], as in the word 'pin', however if it appears word internally, as in 'spin', finally, as in 'cap', or followed by a consonant, as in 'print', it will not have this aspiration.

References:

 * Kazanina, N., Phillips, C., & Idsardi, W. (2006). The Influence of Meaning on the Perception of Speech Sound Contrasts. Proceedings of the National Academy of Sciences USA, 103, 11381-11386. (http://nk.psy.bris.ac.uk/Papers/kazanina-phillips-idsardi_PNAS_2006_reprint.pdf)