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, 323 (5913), 527-30

The Peopling of the Pacific From a Bacterial Perspective

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The Peopling of the Pacific From a Bacterial Perspective

Yoshan Moodley et al. Science.

Abstract

Two prehistoric migrations peopled the Pacific. One reached New Guinea and Australia, and a second, more recent, migration extended through Melanesia and from there to the Polynesian islands. These migrations were accompanied by two distinct populations of the specific human pathogen Helicobacter pylori, called hpSahul and hspMaori, respectively. hpSahul split from Asian populations of H. pylori 31,000 to 37,000 years ago, in concordance with archaeological history. The hpSahul populations in New Guinea and Australia have diverged sufficiently to indicate that they have remained isolated for the past 23,000 to 32,000 years. The second human expansion from Taiwan 5000 years ago dispersed one of several subgroups of the Austronesian language family along with one of several hspMaori clades into Melanesia and Polynesia, where both language and parasite have continued to diverge.

Figures

Fig. 1
Fig. 1
(A) The distribution of H. pylori populations in Asia and the Pacific. The proportions of haplotypes at each sampling location (red numbers; table S1) that were assigned to different bacterial populations are displayed as pie charts whose sizes indicate the numbers of haplotypes. The geographic location of Melanesia and Polynesia is depicted. The term “Austronesia” refers to the entire region inhabited by Austronesian-speaking people from Madagascar through to the Easter Islands. (Inset) A detailed map of Taiwan showing the distribution of aboriginal tribes. The names of the tribes plus the proportion of hspMaori haplotypes among all haplotypes are shown in black at the right. The language-family designations are the same as the tribal names except where indicated by parentheses (EF, East Formosan; MP, Malayo-Polynesian). (B) Phylogenetic relationships among hspMaori strains (80% consensus of 100 ClonalFrame analyses). One haplotype each of hpAsia2 and hspEAsia was used to root the tree. Strains are color-coded according to Austronesian language family in (A). Two black circles within the Pacific clade indicate haplotypes isolated from the Torres Strait islands, and a black triangle among indigenous Taiwanese indicates an hspMaori haplotype from Yami.
Fig. 2
Fig. 2
Global patterns of migration between eight pairs of H. pylori populations as calculated by the isolation with migration model (IMa). (A) Map. The magnitudes of migration are denoted by numbers and arrow thickness and their direction is indicated in blue or red. (B) Graph showing a linear relation between the calibration time (table S2) of six events (filled blue circles) that are dated by archaeological estimates and the estimated time (t). (C) Population tree reconstructed from a consensus of 1000 bootstrap samples from the range of calculated t values to determine the ages of nodes (thousands of years, kyr) associated with the peopling of the Sahul (unfilled circles). Ages (in light blue) are the 95% confidence limits of estimated coalescence times obtained by applying global rate minimum deformation (GRMD) rate-smoothing, as implemented in Treefinder, to the range of t values within the limits of calibration dates.
Fig. 3
Fig. 3
Global phylogeny of H. pylori as calculated by a haplotype approach based on the 80% consensus of 100 ClonalFrame analyses. (A) Phylogenetic tree of divergence time, as indicated by node height versus geographic sources (bottom line) and population assignments (second line). Detailed sources of clades within populations are indicated in the third line from the bottom. Node heights were used to date the two hpSahul nodes (unfilled circles) based on six calibration times (filled blue circles, table S2). Age ranges (light blue numbers) are the 95% confidence limits of estimated coalescence times obtained with GRMD rate-smoothing over the range of node height values and calibration time limits. hpAFR2, hpAfrica2; hpAFR1, hpAfrica1; AM, America. (B) Graph showing a linear relation of calibration time with the range of heights for each node.

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