Institute of Molecular BioSciences, Massey University

Clarke, A.C., Burtenshaw, M.K., McLenachan, P.A., Erickson, D.L., and D. Penny. 2006. Reconstructing the Origins and Dispersal of the Polynesian Bottle Gourd (Lagenaria siceraria). Mol. Biol. Evol. 23(5):893–900.

Abstract: The origin of the Polynesian bottle gourd (Lagenaria siceraria), an important crop species in prehistoric Polynesia, has
remained elusive. Most recently, a South American origin has been favored as the bottle gourd could have been introduced from this continent with the sweet potato by Polynesian voyagers around A.D. 1,000. To test the hypothesis of an American origin for the Polynesian bottle gourd, we developed seven markers specific to bottle gourd (two chloroplast and five nuclear). The nuclear markers were developed using a new technique where polymorphic inter simple sequence repeat (ISSR) markers are converted into single-locus polymerase chain reaction and sequencing markers—an approach that will be useful for developing markers in other taxa. All seven markers were sequenced in 36 cultivars of bottle gourd from Asia, the Americas, and Polynesia. The results support a dual origin for the Polynesian bottle gourd: the chloroplast markers are exclusively of Asian origin, but the nuclear markers show alleles originating in both the Americas and Asia. Because hybridization of Polynesian bottle gourds with post-European introductions cannot be excluded, ancient DNA from archaeological material will be useful for further elucidating the prehistoric movements of this species in Polynesia. This work has implications not only for the dispersal of the Polynesian bottle gourd but also for the domestication and dispersal of the species as a whole.

Hurles, M.E., Matisso-Smith, E., Gray, R.D., and Penny, D. (2003). Untangling Oceanic settlement: the edge of the knowable. Trends in Ecology and Evolution 18(10): 531-540.

Abstract: Human expansion into the far reaches of the Pacific has occurred within the past 3000–4000 years. This is so recent that it is arguably the best opportunity to test models of the origin and dispersal of human groups and their domesticated plants and animals, cultural and linguistic evolution, human impacts on a pristine environment, and the lower limits for a long-term sustainable population. Multidisciplinary research is essential because these models must account for archaeological, ecological, cultural, historical, social, linguistic and (both mitochondrial and nuclear) genetic data. This synthesis has not yet been achieved for any settlement in the world, but there has been considerable progress recently on integrating these disciplines with respect to the settlement of Polynesia.

E. Matisoo-Smith, R. M. Roberts, G.J. Irwin, J.S. Allen, D. Penny. and D.M. Lambert. 1998. Patterns of prehistoric human mobility in Polynesia indicated by mtDNA from the Pacific rat. Proceedings of the National Academy of Sciences, USA. 95: 15145-15150.

Abstract: Human settlement of Polynesia was a major event in world prehistory. Despite the vastness of the distances covered, research suggests that prehistoric Polynesian populations maintained spheres of continuing interaction for at least some period of time in some regions. A low level of genetic variation in ancestral Polynesian populations, genetic admixture (both prehistoric and post-European contact), and severe population crashes resulting from introduction of European diseases make it difficult to trace prehistoric human mobility in the region by using only human genetic and morphological markers. We focus instead on an animal that accompanied the ancestral Polynesians on their voyages. DNA phylogenies derived from mitochondrial control-region sequences of Pacific rats (Rattus exulans) from east Polynesia are presented. A range of specific hypotheses regarding the degree of interaction within Polynesia are tested. These include the issues of multiple contacts between central east Polynesia and the geographically distinct archipelagos of New Zealand and Hawaii. Results are inconsistent with models of Pacific settlement involving substantial isolation after colonization and confirm the value of genetic studies on commensal species for elucidating the history of human settlement.

R. P. Murray-McIntosh, B. J. Scrimshaw, P. J. Hatfield and D. Penny. 1998. Testing migration patterns and estimating founding population size in Polynesia by using human mtDNA sequences. Proceedings of the National Academy of Sciences USA. 95:9047-9052.

Abstract:The hypervariable 1 region of human mtDNA shows markedly reduced variability in Polynesians, and this variability decreases from western to eastern Polynesia. Fifty four sequences from New Zealand Maori show that the mitochondrial variability with just four haplotypes is the lowest of any sizeable human group studied and that the frequency of haplotypes is markedly skewed. The Maori sequences, combined with 268 published sequences from the Pacific, are consistent with a series of founder effects from small populations settling new island groups. The distributions of haplotypes were used to estimate the number of females in founding population of New Zealand Maori. The three-step simulation used a randomly selected founding population from eastern Polynesia, an expansionary phase in New Zealand, and finally the random selection of 54 haplotypes. The results are consistent with a founding population that includes '70 women (between 50 and 100), and sensitivity analysis shows that this conclusion is robust to small changes in haplotype frequencies. This size is too large for models postulating a very small founding population of ‘‘castaways,’’ but it is consistent with a general understanding of Maori oral history as well as the results of recent canoe voyages recreating early trans-oceanic voyages.

D. Penny, M. A. Steel, P. J. Waddell, and M. D. Hendy. 1995. Improved analyses of human mtDNA sequences support a recent African origin for Homo sapiens. Molecular Biology Evolution 12:863-882.

Abstract: New quantitative methods are applied to the 135 human mitochondrial sequences from the Vigilant et al. data set. General problems in analyzing large numbers of short sequences are discussed, and an improved strategy is suggested. A key feature is to focus not on individual trees but on the general “landscape” of trees. Over 1,000 searches were made from random starting trees with only one tree (a local optimum) being retained each time, thereby ensuring optima were found independently. A new tree comparison metric was developed that is unaffected by rearrangements of trees around many very short internal edges. Use of this metric showed that downweighting hypervariable sites revealed more evolutionary structure than studies that weighted all sites equally. Our results are consistent with convergence toward a global optimum. Crucial features are that the best optima show very strong regional differentiation, a common group of 49 African sequences is found in all the best optima, and the best optima contain the 16 !Kung sequences in a separate group of San people. The other 86 sequences form a heterogeneous mixture of Africans, Europeans, Australopapuans, and Asians. Thus all major human lineages occur in Africa, but only a subset occurs in the rest of the world. The existence of these African-only groups strongly contradicts multiregional theories for the origin of Homo sapiens that require widespread migration and interbreeding over the entire range of H. erectus. Only when the multiregional model is rejected is it appropriate to consider the root, based on a single locus, to be the center of origin of a population (otherwise different loci could give alternative geographic positions for the root). For this data, several methods locate the root within the group of 49 African sequences and are thus consistent with the recent African origin of H. sapiens. We demonstrate that the time of the last common ancestor cannot be the time of major expansion in human numbers, and our results are thus also consistent with recent models that differentiate between the last common ancestor, expansion out of Africa, and the major expansion in human populations. Such a two-phase model is consistent with a wide range of molecular and archeological evidence.