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One potential improvement of SP (or more accurately, the TCS software) would be the ability to use the statistical parsimony connection limit to connect the less divergent sequences, followed by use of MP to complete the disconnected networks, as was originally proposed by Templeton et al. [43].
TCS haplotype networks revealed very high levels of population structure with multiple sub-networks failing to connect with the connection limit set to 50 steps.
The individuals from the other five localities are genetically too distinct to be connected within the 95% connection limit (eight steps) and form separate groups, which are not shown.
As several unconnected networks were obtained, we then forced the TCS algorithm to connect all subnetworks with a fixed connection limit of 50 steps.
Separation of populations from the Alafia River from populations in the St . Johns Riveris predicted to have been fairly recent as TCS analysis can connect these two populations within a 95% connection limit.
These samples could not be connected to the others with a 90% parsimony connection limit in the COI+cytB network (the lowest parsimony value allowed by TCS 1.21; Fig. 2A).
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Analyses were run multiple times with varying parsimony connection limits to ascertain the highest limit that would retain each connection.
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