DOI: 10.5061/dryad.tf8q1
title: Data from: Contemporary genetic structure of an endemic freshwater turtle reflects Miocene orogenesis of New Guinea.

description: The island of New Guinea 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 Gondwanal
 origin, occur in New Guinea; all species except one, the endemic Elseya
 novaeguineae, are restricted to the lowlands south of the Central Ranges.
 Elseya novaeguineae is found throughout New Guinea. 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 New Guinea. Its genetic structure bears the
 signature of Miocene vicariance events. The date of the divergence between
 a Birds Head (Kepala Burung) clade and clades north and south of the
 Central Ranges is estimated to be 19.8 Mya [95% highest posterior density
 (HPD) interval of 13.3–26.8 Mya] and the date between the northern and
 southern clades is estimated to be slightly more recent at 17.4 Mya (95%
 HPD interval of 11.0–24.5 Mya). 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 Miocene history of the island of New Guinea,
 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 Langguru Fold Belt;
 (3) the opening of Cenderawasih Bay; and (4) the deep waters of the Aru
 Trough and Cenderawasih Bay that come close to the current coastline to
 maintain isolation of the Birds Head 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 Australian Plate beneath the Pacific Plate.
 Their isolation was probably associated with earlier uplift and drainage
 isolation driven by the accretion of island terranes to the northern
 boundary of the Australian craton that occurred earlier than the oblique
 subduction. The opening of Cenderawasih Bay is too recent (6 Mya) to have
 initiated the isolation of the Birds Head populations from those of the
 remainder of New Guinea, although its deep waters will have served to
 sustain the isolation through successive sea level changes. The molecular
 evidence suggests that the Birds Head docked with New Guinea 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 Miocene, whereas structure within each
 clade across the New Guinea landscape relates to Pliocene and Pleistocene
 times.
description: full_gene_set_12S_16S_CO1_CytB_phylogenyThis nexus file contains the sequence data for the full gene set (ND4, CR, 12s, 16s,Cox1, Cytb) used to confirm major nodes and refine bootstrap support for Elseya novaeguineae, with E. branderhorsti as outgroup.full_gene_set__12S_16S_CO1_CytB_phylogeny.nexreduced_gene_set_CR_ND4_phylogenyThis nexus file contains the sequence data for the reduced gene set (ND4 and CR) used to recover the phylogeny for mitochondrial haplotypes of Elseya novaeguineae, with E. branderhorsti haplotypes as outgroup.nuclear_emydura_group_beast_inputNuclear data in nexus format used as the input for the Beast analysis.mtdna_emydura_group_beast_inputMitochondrial data in nexus format used as the input for the Beast analysis.emydura_group_beast_trees_comb_1-7-5_outputMaximum clade credibility tree saved from figtree from the combined output of our Beast runs.emydura.groupXML file used in the BEAST molecular clock analysis using only the Redbank Plains fossil calibration.