FIGURE 1. Map of the Indonesian-throughflow region.

The main islands, crustal fragments, and other topographic features are labelled. Currently most Indonesian throughflow passes north of Sulawesi, then west of Sulawesi through the Makassar Strait, and finally across the Banda arc. The South Equatorial Current flows along the northern coast of New Guinea and then turns to the east at Halmahera in the Halmahera eddy. We suggest that at 3–5 Myr ago, Halmahera was a much smaller island with most of the area 1,000 m deeper, New Guinea was 2°–3° farther south, and the mountains on the island were also much lower. In addition, Timor was under water, and the Java trench continued eastward and then northward into the Seram trough. Finally, the 'Bird's Head' lay 250–400 km east of its present position with respect to Borneo. Colour indicates elevation relative to mean sea level.