DOI: 10.5061/dryad.gn1v3
title: Data from: A passerine bird's evolution corroborates the geologic history of the island of New Guinea

description: New Guinea is a biologically diverse island, with a unique geologic
 history and topography that has likely played a role in the evolution of
 species. Few island-wide studies, however, have examined the
 phylogeographic history of lowland species. The objective of this study
 was to examine patterns of phylogeographic variation of a common and
 widespread New Guinean bird species (Colluricincla megarhyncha).
 Specifically, we test the mechanisms hypothesized to cause geographic and
 genetic variation (e.g., vicariance, isolation by distance and
 founder-effect with dispersal). To accomplish this, we surveyed three
 regions of the mitochondrial genome and a nuclear intron and assessed
 differences among 23 of the 30 described subspecies from throughout their
 range. We found support for eight highly divergent lineages within C.
 megarhyncha. Genetic lineages were found within continuous lowland habitat
 or on smaller islands, but all individuals within clades were not
 necessarily structured by predicted biogeographic barriers. There was some
 evidence of isolation by distance and potential founder-effects.
 Mitochondrial DNA sequence divergence among lineages was at a level often
 observed among different species or even genera of birds (5-11%),
 suggesting lineages within regions have been isolated for long periods of
 time. When topographical barriers were associated with divergence
 patterns, the estimated divergence date for the clade coincided with the
 estimated time of barrier formation. We also found that dispersal distance
 and range size are positively correlated across lineages. Evidence from
 this research suggests that different phylogeographic mechanisms
 concurrently structure lineages of C. megarhyncha and are not mutually
 exclusive. These lineages are a result of evolutionary forces acting at
 different temporal and spatial scales concordant with New Guinea’s
 geological history.
description: C_megar_mtDNAlignmentThis is a sequence alignment of concatenated mtDNA genes used for estimating the maximum likelihood tree.C_megar_nDNAphasedalignmentThis is a sequence alignment of phase data from the AR35 nuclear gene.C_megar_mtDNA_ArlequinInput file used for analysis in Arlequin with population structure section.C_megar_nDNA_ArlequinInput file used for analysis in Arlequin.C_megar_mtDNA_networkInput file used for estimating haplotype network.C_megar_nDNA_networkInput file used for estimating the nuclear allele network.C_megar_mtDNABestTreePhylomapperTree used for estimation of evolution in dispersal distance.C_megar_Locations_phylomapperLatitude and longitude positions of each sample used for estimation of evolution in dispersal distances.BB_SPBRaw sequence data that was used to phase nuclear alleles. These are for the basins Bintuni and South Papua.CapeVRaw sequence data that was used to phase nuclear alleles. These are for the basin Cape Vogel.EIRaw sequence data that was used to phase nuclear alleles. These are for the eastern islands.MBRaw sequence data that was used to phase nuclear alleles. These are for the basin Meervlakte.SPPRaw sequence data for nuclear alleles that were phased. The are sequences from the basin South Papuan Peninsula.SRBRaw sequence data for nuclear alleles that were phased. The are sequences from the basin Sepik Ramu.TFRaw sequence data for nuclear alleles that were phased. The are sequences from the basin Trans-fly.READMEFILEThis readme file describes all the data files in this package. It is also available for download alongside each file.