Table 1. Summary of results from D. melanogaster to D. triauraria liftover analysis.

Percentages of “Unique lifted-over to D. triauraria” represent number out of total boundaries or domains. Percentages of orthologous, non-orthologous, and subcategories of boundaries and domains represent number out of “Unique lifted-over to D. triauraria”. Truncated and expanded domains do not meet the 90% reciprocal overlap criterion due to large insertion/deletion mutations that have created asymmetry in TAD size between the two species. Missing boundaries and domains are those that could not be lifted-over to D. triauraria.

Category	Boundaries	Domains
Total in D. melanogaster	701	552
Unique lifted-over to D. triauraria	654 (93%)	544 (99%)
Orthologous	473 (72%)	134 (25%)
Non-orthologous	181 (28%)	410 (75%)
Non-orthologous (truncated/expanded)	–	82 (15%)
Non-orthologous (split by lineage-specific boundary)	–	104 (19%)
Non-orthologous (split by rearrangement)	–	224 (41%)
Missing	47	8