Dispersal ghosts in Oceania

Pharmacogenomics in Papua New Guineans: unique profiles and implications for enhancing drug efficacy while improving drug safety

Papua New Guinea (PNG) can be roughly divided into highland, coastal and island peoples with significant mitochondrial DNA differentiation reflecting early and recent distinct migrations from Africa and East Asia, respectively. Infectious diseases such as tuberculosis, malaria and HIV severely impact on the health of its peoples for which drug therapy is the major treatment and pharmacogenetics has clinical relevance for many of these drugs. Although there is generally little information about known single nucleotide polymorphisms in the population, in some instances, their frequencies have been shown to be higher than anywhere worldwide. For example, CYP2B6*6 is over 50%, and CYP2C19*2 and *3 are over 40 and 25%, respectively. Conversely, CYP2A6*9, 2B6*2, *3, *4 and *18, and 2C8*3 appear to be much lower than in Whites. CYP2D6 known variants are unclear, and for phase II enzymes, only UGT2B7 and UGT1A9 data are available, with variant frequencies either slightly lower than or similar to Whites. Although almost all PNG people tested are rapid acetylators, but which variant(s) define this phenotype is not known. For HLA-B*13:01, HLA-B*35:05 and HLA-C*04:01, the frequencies show some regioselectivity, but the clinical implications with respect to adverse drug reactions are not known. There are minimal phenotype data for the CYPs and nothing is known about drug transporter or receptor genetics. Determination of genetic variants that are rare in Whites or Asians but common in PNG people is a topic of both scientific and clinical importance, and further research needs to be carried out. Optimizing the safety and efficacy of infectious disease drug therapy through pharmacogenetic studies that have translation potential is a priority.

How much impact do gains in height have on shoulder breadths within Taiwanese families?

OBJECTIVES

This study investigates allometric changes in shoulder breadths relative to changes in stature arising from rapidly changing developmental circumstances within 107 Taiwanese families. It speaks to broader issues related to the extent of phenotypic plasticity of body breadths humans are capable of in response to reductions in developmental stressors.

METHODS

An examination of relationships between shoulder breadth and height within individuals in each generation was followed by evaluation of patterns of difference between same-sex parent-offspring pairs in height and shoulder breadth.

RESULTS

Height was similarly positively correlated with shoulder breadth within fathers, mothers, sons, and daughters (P ≤ 0.002). Variance accounted for ranged from an adjusted R² of 0.201 among fathers to 0.151 for sons, with mothers' and daughters' values being 0.187 and 0.181, respectively. Comparisons of differences within families indicate that parents who were shorter than their same-sex offspring also tended to have modestly narrower biacromial breadths (father-son pairs: adjusted R²  = 0.112; t = 2.82, P = .007; mother-daughter pairs: adjusted R²  = 0.135; t = 2.97, P = 0.005).

CONCLUSIONS

Taken as a whole, results here support the view that secular changes in stature are not accompanied by similar changes in body breadths, perhaps so that responses to developmental environmental improvements do not alter thermoregulatory equilibria that reflect long-term evolutionary processes. These results indirectly constrain plausible hypotheses about how ancestors of Austronesian speakers altered their body size and shape as they voyaged to Fiji, Western Polynesia, and beyond.

Craniofacial evolution in Polynesia: a geometric morphometric study of population diversity

OBJECTIVES

This study tests differences in craniofacial size and shape attributed to demographic history and plastic responses to differing environments in the islands of Polynesia. The dispersal of modern humans into Polynesia provides a useful scenario to investigate the impact of migration on human craniofacial diversity.

METHODS

Three dimensional geometric morphometric techniques are used to examine morphological diversity within Oceanic population samples. The importance of geographic and climatic variables is quantified by partial linear regression.

RESULTS

The results show a homogeneous Polynesian morphology grouping in relation to neighboring regions. There is, however, considerable diversity within the Polynesian samples themselves. Natural selection due to environmental differences is not an important factor in the patterns of craniofacial diversity found in the samples.

CONCLUSIONS

Historical patterns such as migration and population isolation influence patterns of craniofacial morphology within Polynesia, and our results demonstrate that morphological diversity can evolve in populations isolated for a relatively short period of time.

Ancient migration routes of Austronesian-speaking populations in oceanic Southeast Asia and Melanesia might mimic the spread of nasopharyngeal carcinoma

Mitochondrial DNA (mtDNA) and non-recombining Y chromosome (NRY) are inherited uni-parentally from mother to daughter or from father to son respectively. Their polymorphism has initially been studied throughout populations of the world to demonstrate the "Out of Africa" hypothesis. Here, to correlate the distribution of nasopharyngeal carcinoma (NPC) in different populations of insular Asia, we analyze the mtDNA information (lineages) obtained from genotyping of the hyper variable region (HVS I & II) among 1400 individuals from island Southeast Asia (ISEA), Taiwan and Fujian and supplemented with the analysis of relevant coding region polymorphisms. Lineages that best represented a clade (a branch of the genetic tree) in the phylogeny were further analyzed using complete genomic mtDNA sequencing. Finally, these complete mtDNA sequences were used to construct a most parsimonious tree which now constitutes the most up-to-date mtDNA dataset available on ISEA and Taiwan. This analysis has exposed new insights of the evolutionary history of insular Asia and has strong implications in assessing possible correlations with linguistic, archaeology, demography and the NPC distribution in populations within these regions. To obtain a more objective and balanced genetic point of view, slowly evolving biallelic Y single nucleotide polymorphism (Y-SNP) was also analyzed. As in the first step above, the technique was first applied to determine affinities (macro analysis) between populations of insular Asia. Secondly, sixteen Y short tandem repeats (Y-STR) were used as they allow deeper insight (micro analysis) into the relationship between individuals of a same region. Together, mtDNA and NRY allowed a better definition of the relational, demographic, cultural and genetic components that constitute the make up of the present day peoples of ISEA. Outstanding findings were obtained on the routes of migration that occurred along with the spread of NPC during the settlement of insular Asia. The results of this analysis will be discussed using a conceptual approach.

Extreme patterns of variance in small populations: placing limits on human Y-chromosome diversity through time in the Vanuatu Archipelago

Small populations are dominated by unique patterns of variance, largely characterized by rapid drift of allele frequencies. Although the variance components of genetic datasets have long been recognized, most population genetic studies still treat all sampling locations equally despite differences in sampling and effective population sizes. Because excluding the effects of variance can lead to significant biases in historical reconstruction, variance components should be incorporated explicitly into population genetic analyses. The possible magnitude of variance effects in small populations is illustrated here via a case study of Y-chromosome haplogroup diversity in the Vanuatu Archipelago. Deme-based modelling is used to simulate allele frequencies through time, and conservative confidence bounds are placed on the accumulation of stochastic variance effects, including diachronic genetic drift and contemporary sampling error. When the information content of the dataset has been ascertained, demographic models with parameters falling outside the confidence bounds of the variance components can then be accepted with some statistical confidence. Here I emphasize how aspects of the demographic history of a population can be disentangled from stochastic variance effects, and I illustrate the extreme roles of genetic drift and sampling error for many small human population datasets.

Unexpected NRY chromosome variation in Northern Island Melanesia

To investigate the paternal population history of populations in Northern Island Melanesia, 685 paternally unrelated males from 36 populations in this region and New Guinea were analyzed at 14 regionally informative binary markers and 7 short tandem repeat (STR) loci from the nonrecombining portion of the Y chromosome. Three newly defined binary markers (K6-P79, K7-P117, and M2-P87) aided in identifying considerable heterozygosity that would have otherwise gone undetected. Judging from their geographic distributions and network analyses of their associated STR profiles, 4 lineages appear to have developed in this region and to be of considerable age: K6-P79, K7-P117, M2-P87, and M2a-P22. The origins of K5-M230 and M-M4 are also confirmed as being located further west, probably in New Guinea. In the 25 adequately sampled populations, the number of different haplogroups ranged from 2 in the single most isolated group (the Aita of Bougainville), to 9, and measures of molecular diversity were generally not particularly low. The resulting pattern contradicts earlier findings that suggested far lower male-mediated diversity and gene exchange rates in the region. However, these earlier studies had not included the newly defined haplogroups. We could only identify a very weak signal of recent male Southeast Asian genetic influence (<10%), which was almost entirely restricted to Austronesian (Oceanic)-speaking groups. This contradicts earlier assumptions on the ancestral composition of these groups and requires a revision of hypotheses concerning the settlement of the islands of the central Pacific, which commenced from this region.