Table 3. Comparison of the utility of various complimentary nuclear markers for species diagnosis in the ponerine ants of the Malagasy.

Taxa	18S	28S	ITS1	Comments
Anochetus goodmani	Intra – no variation. Inter – 2 bp from A. boltoni, and 3 bp from O. troglodytes, O. coquereli	Intra – no variation across north Inter – >15 bp divergent from A. madagascarensis.	Intra – extreme variation (length and substitution) across range. Some corresponding to deep CO1 splits – provisionally orthologous. However, deep paralogous divergences have been sequenced within single individuals through different amplifications and extractions.	rRNA is, a priori, difficult to differentiate orthologous from paraologous. Not as immediately useful as an independent marker without cloning.
Anochetus boltoni	Intra – no variation. Inter – 2 bp from A. goodmani, 2 bp from O. troglodytes and no difference from O. coquereli.	N/A	Intraspecific variation of 1% (indels and substitutions) between the two sampled populations.
Anochetus madagascarensis	N/A	Intra – no variation. Inter – >15 bp divergent from A. goodmani.	Intra – variation that does NOT reflect CO1 variation.	rRNA is, a priori, difficult to differentiate orthologous from paraologous. Not as immediately useful as an independent marker without cloning. -Positive Wolbachia test.
Anochetus grandidieri	N/A	N/A	Low intraspecific variation that does reflect CO1 geographic variation.	- Positive Wolbachia test.
Anochetus pattersoni	N/A	N/A	N/A
Odontomachus coquereli	Intra – no variation. Inter – 2 bp from O. troglodytes. 2 bp from A. boltoni, and 3 bp from A. goodmani.	Intra – variation. Large variation at geographically distal ends of distribution. Inter – differentiates between three Malagasy species.	Intraspecific variation that only partially reflects geography and CO1 variation – while some clearly does not. Paralogous and orthologous
Odontomachus troglodytes	Intra – no variation. Inter – 2 bp from O. coquereli. 3 bp from A. boltoni, and 3 bp from A. goodmani.	Intra – some variation that does not correspond to geography or CO1. Inter – does not differentiate between O. simillimus	Intraspecific variation that only partially reflects geography and CO1 variation	All specimens tested positive for Wolbachia.
Odontomachus simillimus	N/A	Intra – no variation. Inter – does not differentiate O. troglodytes	N/A