Complete mtDNA from Filipino groups

European Journal of Human Genetics, (12 June 2013) | doi:10.1038/ejhg.2013.122

Complete mtDNA genomes of Filipino ethnolinguistic groups: a melting pot of recent and ancient lineages in the Asia-Pacific region

Frederick Delfin et al.

The Philippines is a strategic point in the Asia-Pacific region for the study of human diversity, history and origins, as it is a cross-road for human migrations and consequently exhibits enormous ethnolinguistic diversity. Following on a previous in-depth study of Y-chromosome variation, here we provide new insights into the maternal genetic history of Filipino ethnolinguistic groups by surveying complete mitochondrial DNA (mtDNA) genomes from a total of 14 groups (11 groups in this study and 3 groups previously published) including previously published mtDNA hypervariable segment (HVS) data from Filipino regional center groups. Comparison of HVS data indicate genetic differences between ethnolinguistic and regional center groups. The complete mtDNA genomes of 14 ethnolinguistic groups reveal genetic aspects consistent with the Y-chromosome, namely: diversity and heterogeneity of groups, no support for a simple dichotomy between Negrito and non-Negrito groups, and different genetic affinities with Asia-Pacific groups that are both ancient and recent. Although some mtDNA haplogroups can be associated with the Austronesian expansion, there are others that associate with South Asia, Near Oceania and Australia that are consistent with a southern migration route for ethnolinguistic group ancestors into the Asia-Pacific, with a timeline that overlaps with the initial colonization of the Asia-Pacific region, the initial colonization of the Philippines and a possible separate post-colonization migration into the Philippine archipelago.

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Dual origins of cultivated coconuts

PLoS ONE 6(6): e21143. doi:10.1371/journal.pone.0021143

Independent Origins of Cultivated Coconut (Cocos nucifera L.) in the Old World Tropics

Bee F. Gunn et al.

As a portable source of food, water, fuel, and construction materials, the coconut (Cocos nucifera L.) played a fundamental role in human migrations and the development of civilization across the humid tropics. Here we investigated the coconut's domestication history and its population genetic structure as it relates to human dispersal patterns. A sample of 1,322 coconut accessions, representing the geographical and phenotypic diversity of the species, was examined using ten microsatellite loci. Bayesian analyses reveal two highly genetically differentiated subpopulations that correspond to the Pacific and Indo-Atlantic oceanic basins. This pattern suggests independent origins of coconut cultivation in these two world regions, with persistent population structure on a global scale despite long-term human cultivation and dispersal. Pacific coconuts show additional genetic substructure corresponding to phenotypic and geographical subgroups; moreover, the traits that are most clearly associated with selection under human cultivation (dwarf habit, self-pollination, and “niu vai” fruit morphology) arose only in the Pacific. Coconuts that show evidence of genetic admixture between the Pacific and Indo-Atlantic groups occur primarily in the southwestern Indian Ocean. This pattern is consistent with human introductions of Pacific coconuts along the ancient Austronesian trade route connecting Madagascar to Southeast Asia. Admixture in coastal east Africa may also reflect later historic Arab trading along the Indian Ocean coastline. We propose two geographical origins of coconut cultivation: island Southeast Asia and southern margins of the Indian subcontinent.

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The spread of Austronesian farmers across the Pacific

This is the first of three interesting papers that appear ahead of print in Current Anthropology. Peter Bellwood reviews the spread of farming across the Pacific from its two sources (China including Taiwan, and the New Guinea highlands).

Related:

• Major East-West divide in Indonesian Y chromosomes
• More on geographical divide between Asian and Melanesian types in Indonesia (Cox et al. 2010)
• Demographic history of Oceania (Wollstein et al. 2010)

Current Anthropology http://www.jstor.org/stable/full/10.1086/658181

Holocene Population History in the Pacific Region as a Model for Worldwide Food Producer Dispersals

Peter Bellwood

Pacific prehistory (excluding Australia) since 3000 BC reflects the impacts of two source regions for food production: China from the Yangzi southward (including Taiwan) and the western Pacific (especially the New Guinea Highlands). The linguistic (Austronesian, Trans–New Guinea), bioanthropological/human genetic, and Neolithic archaeological records each carry signals of expansion from these two source regions. A combined consideration of the multiregional results within all three disciplines (archaeology, linguistics, and biology) offers a historical perspective that will never be obtained from one discipline or one region alone. The fundamental process of human behavior involved in such expansion—population dispersal linked to increases in human population size—is significant for explaining the early spreads of food production and language families in many parts of the world. This article is concerned mainly with the archaeological record for the expansion of early food producers, Austronesian languages, and Neolithic technologies through Taiwan into the northern Philippines as an early stage in what was to become the greatest dispersal of an ethnolinguistic population in world history before AD 1500.

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Bacteria and the human peopling of the Pacific

A new paper in Science looks at the peopling of the Pacific from the perspective of genetic diversity of the bacterium H. pylori which is found in people's stomachs.

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

Science doi:10.1126/science.1166083

The Peopling of the Pacific from a Bacterial Perspective

Yoshan Moodley et al.

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.

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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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