European admixture on the Micronesian island of Kosrae

Kosrae has a population of about 7 thousand, so the finding that most of the European ancestry in this population can be traced to one 19th c. European individual, shows the reality of reproductive inequality I mentioned in a previous post.

European Journal of Human Genetics advance online publication 21 October 2009; doi: 10.1038/ejhg.2009.180

European admixture on the Micronesian island of Kosrae: lessons from complete genetic information

Penelope E Bonnen et al.

Abstract

The architecture of natural variation present in a contemporary population is a result of multiple population genetic forces, including population bottleneck and expansion, selection, drift, and admixture. We seek to untangle the contribution of admixture to genetic diversity on the Micronesian island of Kosrae. Toward this goal, we used a complete genetic approach by combining a dense genome-wide map of 100 000 single-nucleotide polymorphisms (SNPs) with data from uniparental markers from the mitochondrial genome and the nonrecombining portion of the Y chromosome. These markers were typed in 3200 individuals from Kosrae, representing 80% of the adult population of the island. We developed novel software that uses SNP data to delineate ancestry for individual segments of the genome. Through this analysis, we determined that 39% of Kosraens have some European ancestry. However, the vast majority of admixed individuals (77%) have European alleles spanning less than 10% of their genomes. Data from uniparental markers show most of this admixture to be male, introduced in the late nineteenth century. Furthermore, pedigree analysis shows that the majority of European admixture on Kosrae is because of the contribution of one individual. This approach shows the benefit of combining information from autosomal and uniparental polymorphisms and provides new methodology for determining ancestry in a population.

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Bayesian phylogenetics of languages and the timing of Austronesian settlement of the Pacific from Taiwan

The same Bayesian methodology was used by the first author to conclude that the spread of Indo-European languages began in Asia Minor during the Neolithic.



From the paper:

The innovationist "pulse-pause" scenario posits that the Austronesians originated in Taiwan around 5500 years ago and spread through the Pacific in a sequence of expansion pulses and settlement pauses (2, 4–6).

...

The divergence time estimates for the age of the Austronesian language family support the pulse-pause scenario (Fig. 2). The estimated root age of Austronesian across all the post–burn-in trees has a mean of 5230 years [95% highest posterior density (HPD) interval, 4750 to 5800 years B.P.). The divergence time estimates were robust across a range of calibrations and different models (28).

The concordance of Bayesian linguistics with the pulse-pause archaeological model is remarkable. So, how was the slow-boat model supported in the first place?

In contrast, proponents of the slow-boat scenario argue that the Austronesians emerged from an extensive sociocultural network of maritime exchange in Wallacea (in the region of modern day Sulawesi and the Moluccas) around 13,000 to 17,000 years B.P. based on the dating of mitochondrial lineages (11, 12).

...

Our estimates for the age of the Austronesian expansion are considerably younger than the deep age estimates of the slow-boat scenario (11, 12, 15). One possibility is that these deep estimates are artifacts due to problems with accurately dating genetic change. There is increasing evidence that rates of genetic change estimated over thousands of years are substantially higher than the long-term substitution rate (21). This violation of the molecular clock leads to the systematic overestimation of recent divergence times.

The problem was that a calibrated evolutionary mutation rate was used to estimate these ages, making them about 3 times older than the Austronesian expansion. Sound familiar?

Science DOI: 10.1126/science.1166858

Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement

R. D. Gray et al.

Abstract

Debates about human prehistory often center on the role that population expansions play in shaping biological and cultural diversity. Hypotheses on the origin of the Austronesian settlers of the Pacific are divided between a recent "pulse-pause" expansion from Taiwan and an older "slow-boat" diffusion from Wallacea. We used lexical data and Bayesian phylogenetic methods to construct a phylogeny of 400 languages. In agreement with the pulse-pause scenario, the language trees place the Austronesian origin in Taiwan approximately 5230 years ago and reveal a series of settlement pauses and expansion pulses linked to technological and social innovations. These results are robust to assumptions about the rooting and calibration of the trees and demonstrate the combined power of linguistic scholarship, database technologies, and computational phylogenetic methods for resolving questions about human prehistory.

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