Contemporary genetic structure of an endemic freshwater turtle reflects M iocene orogenesis of N ew G uinea

The island of N ew G uinea lies in one of the most tectonically active regions in the world and has long provided outstanding opportunity for studies of biogeography. Several chelid turtles, of clear G ondwanal origin, occur in N ew G uinea; all species except one, the endemic E lseya novaeguineae , are restricted to the lowlands south of the Central Ranges. E lseya novaeguineae is found throughout N ew G uinea. We use mitochondrial and nuclear gene variation among populations of E . novaeguineae throughout its range to test hypotheses of recent extensive dispersal versus more ancient persistence in N ew G uinea. Its genetic structure bears the signature of M iocene vicariance events. The date of the divergence between a B irds H ead ( K epala B urung) clade and clades north and south of the Central Ranges is estimated to be 19.8  M ya [95% highest posterior density ( HPD) interval of 13.3–26.8  M ya] and the date between the northern and southern clades is estimated to be slightly more recent at 17.4  M ya (95% HPD interval of 11.0–24.5  M ya). The distribution of this endemic species is best explained by persistent occupation (or early invasion and dispersal) and subsequent isolation initiated by the dramatic landform changes that were part of the M iocene history of the island of N ew G uinea, rather than as a response to the contemporary landscape of an exceptionally effective disperser. The driving influence on genetic structure appears to have been isolation arising from a combination of: (1) the early uplift of the Central Ranges and establishment of a north‐south drainage divide; (2) development of the L angguru F old B elt; (3) the opening of C enderawasih B ay; and (4) the deep waters of the A ru T rough and C enderawasih B ay that come close to the current coastline to maintain isolation of the B irds H ead through periods of sea level minima (−135 m). The dates of divergence of turtle populations north and south of the ranges predate the telescopic uplift of the central ranges associated with oblique subduction of the A ustralian P late beneath the P acific P late. Their isolation was probably associated with earlier uplift and drainage isolation driven by the accretion of island terranes to the northern boundary of the A ustralian craton that occurred earlier than the oblique subduction. The opening of C enderawasih B ay is too recent (6 M ya) to have initiated the isolation of the B irds H ead populations from those of the remainder of N ew G uinea, although its deep waters will have served to sustain the isolation through successive sea level changes. The molecular evidence suggests that the B irds H ead docked with N ew G uinea some time before the Central Ranges emerged as a barrier to turtle dispersal. Overall, deep genetic structure of the species complex reflects events and processes that occurred during M iocene, whereas structure within each clade across the N ew G uinea landscape relates to Pliocene and Pleistocene times. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society , 2014, 111 , 192–208.