Complex sentence: The nature of parapatry implies a partial extrinsic barrier during divergence, thus leading to a difficulty in determining whether parapatric speciation actually occurred, or if an alternative mode (notably, allopatric speciation) can explain the data.
Split into simpler sentences: The nature of parapatry implies a partial extrinsic barrier during divergence. This leads to a complication in determining whether parapatric speciation actually occurred, or if an alternative mode (notably, allopatric speciation) can explain the data.