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Map outlining migratory paths of Austronesian speaking populations, including estimated dates. Adapted from Bellwood et al ., (2011) [52]. doi:10.1371/journal.pone.0035026.g001 

Map outlining migratory paths of Austronesian speaking populations, including estimated dates. Adapted from Bellwood et al ., (2011) [52]. doi:10.1371/journal.pone.0035026.g001 

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The high risk of metabolic disease traits in Polynesians may be partly explained by elevated prevalence of genetic variants involved in energy metabolism. The genetics of Polynesian populations has been shaped by island hoping migration events which have possibly favoured thrifty genes. The aim of this study was to sequence the mitochondrial genome...

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... evidence from linguistics, archaeology and genetics indicates that the Maori population of New Zealand (NZ) represents the final link in a long chain of island-hopping voyages by Polynesians, which began in Taiwan and stretched through Melanesia and across the Pacific Islands over a period of 5–6000 years ( Figure 1). Around 800 years ago one or more small groups of voyagers arrived in NZ from Tahiti, via the Cook Islands. This event marked the last of the great human migrations and the creation of an isolated founder population. The widespread intermarriage between Maoris and Europeans over the past 200 years (8–10 generations) has introduced substantial European genomic ancestry ( , 40%) into the contemporary Maori gene pool [1]. Maoris, and Polynesians more generally, are disproportionately affected with certain metabolic disease traits eg. obesity and type 2 diabetes mellitus [2,3,4,5]. Given that these traits are partially influenced by genetic factors it is likely that genes involved in energy metabolism play a role in disease risk [6]. Mitochondrial genes could potentially account for some of the high prevalence of metabolic disease traits in Maoris. Coding variants in mitochondrial genes that exhibit unusually high frequencies in Maori may have been driven to high frequency by positive selection due to periods of feast and famine during the migrations (ie. thrifty genes) [7]. Alternatively, these mitochondrial variants may have simply increased in frequency in Maoris via genetic drift as a consequence of repeated founder events and subsequent population bottlenecks. Complete mitochondrial genome sequence data have been previously investigated to elucidate the evolutionary history among human populations around the world [8]. Studies have also comprehensively investigated mitochondrial genome variation in relation to metabolic syndrome traits [9,10]. However, no complete mitochondrial genome surveys have involved a Maori sample and Polynesians more generally have been under- represented. Given the unusual maternal history of Maoris it is likely that a unique mitochondrial genomic makeup exists in this Polynesian subgroup. In this study we sequenced the entire mitochondrial genome in a group of Maori individuals and performed population genetic analyses to characterise the patterns of genomic variation in this Polynesian population. These new data provide the opportunity to enhance the phylogenetic picture of the mitochondrial genome in the South Pacific region and establish a foundation for future studies of mitochondrial DNA and metabolic disease traits in Polynesian populations. A summary of mitochondrial (mt) sequence variation for all 20 Maori mtDNA genomes is shown in Table 1. These sequences are the only complete NZ Maori sequences currently available (at time of writing). Previous studies have suggested that there is very limited mtDNA variation in Polynesians in general, and even less in Maori [11,12] and no Maori-specific genetic mtDNA markers have yet been identified. Sequence variation was identified by comparison against the revised Cambridge Reference Sequence (CRS) [13], which belongs to haplogroup H (commonly found in European peoples). The mt sequence variation identified in the Maori individuals differed from the CRS at 44 variable sites (see Table 1). Of these variant sites, 22 were fixed in all 20 Maori individuals – these are the defining markers of mitochondrial haplogroup B, and its further substructure (haplotypes) such as B4a1a1, to which Maoris belong. There were 12 singleton variants identified and a further 10 variants were shared by two or more individuals and define subclades within the Maori mtDNA phylogeny. The limited sequence variation was validated by calculation of h and p diversity statistics in DNAspV5 [14]. Table 2 shows the amount of DNA sequence diversity of 189 complete mtDNA sequences as well as diversity within each specific population. The Maori group were found to exhibit high haplotype diversity (h = 0.92), yet diversity was substantially lower than that seen in any of the other three populations (see Table 2). When looking at the nucleotide ( p ) diversity it can be seen that Maoris exhibit a value 10-fold lower ( p = 0.00018) compared to that of the other populations. As expected there is no maternal European admixture identified in this group. All mtDNA sequences are clearly Polynesian (Maori) and show the characteristic, and well documented, Polynesian Motif markers [15,16]: 16189, 16217, 16247, and 16261 (see Table 1). Phylogenetic analysis of the Maori sequences in the software mtPhy [17] confirmed that all 20 belong to haplogroup B. As expected from previous studies of the Hyper Variable Region (HVR) in Polynesians [11,12,15,18,19], these Maori sequences all group deep within haplogroup B (for reference see Phylotree [20]). To further investigate the sub-structure of haplogroup B a detailed phylogeny was reconstructed to include 64 complete sequences representing B4a (10 Asian, 14 Taiwanese, 4 Coastal PNG, 16 Pacific Islanders and 20 Maori). Figure 2 illustrates this tree (Asian/Austronesian mt DNA sequences) and shows that all 20 Maori sequences group within B4a1a1, with Pacific Islander and Coastal PNG (Melanesian) mt sequences. These groupings fit well with previous mtDNA work [18,19,21,22,23,24], and complement the hypothetical model of Polynesian origin stemming from Taiwan [25]. Apart from the variants which define haplogroup B, we have identified three novel Polynesian (Maori) haplotypes – until now all documented Polynesian mt haplotypes have been B4a1a1a. Table 3 displays the frequency and specific markers for the haplotypes identified in the 20 complete Maori mt sequences. The most interesting haplotype, B4a1a1a3 (unpublished data), was recently included in an updated build of Phylotree (. phylotree.org/ [20]). This haplotype was present in 35% (n = 7) of the individuals sequenced, and is defined by the variants 1185T and 4769A. This study has identified six novel (undocumented) mtDNA variants in the Maori sample: five within protein coding regions and one in the control region (see Table 4). An extended database search of mtDB [26] and Mitomap [27] and for these variants returned no hits, thus these positions are deemed to be novel. Two variants result in amino acid sequence changes; 9255T (Pro R Ser) and 15014C (Phe R Leu). Apart from variant 3909T, the novel variants were only noted in individuals and are not present in the wider population and are thus probably sporadic, rather than ...

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... A general overview of Austronesian population movements. This global map was developed from one first shown in Bellwood et al. (2011) and is taken from Benton et al. (2012). It shows the global spread of Austronesian people with routes and dates as known at that time. ...
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The Austronesian Diaspora is a 5,000-year account of how a small group of Taiwanese farmers expanded to occupy territories reaching halfway around the world. Reconstructing their detailed history has spawned many academic contests across many disciplines. An outline orthodox version has eventually emerged but still leaves many unanswered questions. The remarkable power of whole-genome technology has now been applied to people across the entire region. This review gives an account of this era of genetic investigation and discusses its many achievements, including revelation in detail of many unexpected patterns of population movement and the significance of this information for medical genetics.
... A general overview of Austronesian population movements. This global map was developed from one first shown inBellwood et al. (2011) is taken fromBenton et al. (2012).It shows the global spread of Austronesian people with routes and dates as known at that time. Its purpose is to present a picture of the 5000-year expansion of Austronesian-speaking people from a focal origin in mainland south east Asia to Madagascar in the west to Columbia in the east. ...
Article
The Austronesian Diaspora is a 5000-year account of how a small group of Taiwanese farmers expanded to occupy territories reaching halfway round the world. Reconstructing their detailed history has spawned many academic contests across many disciplines. An outline orthodox version has eventually emerged, but still leaves many unanswered questions. The remarkable power of whole-genome technology has now been applied to people across the entire region. This review gives an account of this era of genetic investigation and discusses its many achievements including revelation in detail of many unexpected patterns of population movement and the significance of this information for medical genetics.
... To investigate the phylogenetic relationships between the mitogenomes of the ancient and modern Tokelauans, we obtained other publicly available Pacific mitochondrial sequences from GenBank (Duggan et al. 2014;Duggan and Stoneking 2013;Benton et al. 2012;Hudjashov et al. 2018;Brandão et al. 2016) (See Supplemental Table 6). These data include sequences from West Polynesia (Tuvalu, Niue, Tonga, Samoa), East Polynesia (Cook Islands, Leeward Society Islands, and New Zealand), Northern Polynesian Outliers (Ontong Java, Bellona, Rennell, and Tikopia) and Micronesia (Kiribati, Nauru, Kapingamarangi, and Majuro). ...
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Tokelau is a remote archipelago of atolls in western Polynesia, located approximately 500 km north of Samoa. It is thought to have been settled as part of the Austronesian expansion(s). However, its exact role in this population dispersal is not completely understood. Here we describe the results of complete mitochondrial genome sequencing for both the current inhabitants and ancient individuals from the archipelago in addition to an assessment of Y-chromosome diversity among the present population. We find relatively little genetic diversity compared with other western Polynesian populations, most likely due to historically reported bottleneck events. However, the presence of rare mitochondrial lineages hints at prehistoric occupation by peoples from the northwest (e.g., Tuvalu and Micronesia). Ancient DNA data from Atafu, the northernmost Tokelauan atoll, is further consistent with abandonment and later resettlement of the island from a Samoan or Samoan-derived source population. Moreover, the ancient and modern mitogenomes also suggest links with other atoll populations in the western Pacific.
... Dental samples and SHSU bone samples were amplified at 100 pg inputs; PSU bone samples were amplified at~8000 mtDNA copies. Hair and buccal swabs were extracted with PrepFiler forensic DNA extraction kit (Thermo Fisher, Waltham, MA, USA), and the protocol described by Gallimore et al. was followed for hair samples [33]. ...
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Forensic mitochondrial DNA (mtDNA) analysis conducted using next-generation sequencing (NGS), also known as massively parallel sequencing (MPS), as compared to Sanger-type sequencing brings modern advantages, such as deep coverage per base (herein referred to as read depth per base pair (bp)), simultaneous sequencing of multiple samples (libraries) and increased operational efficiencies. This report describes the design and developmental validation, according to forensic quality assurance standards, of end-to-end workflows for two multiplexes, comprised of ForenSeq mtDNA control region and mtDNA whole-genome kits the MiSeq FGxTM instrument and ForenSeq universal analysis software (UAS) 2.0/2.1. Polymerase chain reaction (PCR) enrichment and a tiled amplicon approach target small, overlapping amplicons (60–150 bp and 60–209 bp for the control region and mtGenome, respectively). The system provides convenient access to data files that can be used outside of the UAS if desired. Studies assessed a range of environmental and situational variables, including but not limited to buccal samples, rootless hairs, dental and skeletal remains, concordance of control region typing between the two multiplexes and as compared to orthogonal data, assorted sensitivity studies, two-person DNA mixtures and PCR-based performance testing. Limitations of the system and implementation considerations are discussed. Data indicated that the two mtDNA multiplexes, MiSeq FGx and ForenSeq software, meet or exceed forensic DNA quality assurance (QA) guidelines with robust, reproducible performance on samples of various quantities and qualities.
... Despite this, the limited research undertaken to date indicates that genomes of individuals and populations with Māori ancestry are significantly different from western European and Asian genomes. [21][22][23] Moreover, there is evidence for differences between Eastern (Cook Island Māori, Hawaiian, Tahitian and Aotearoa New Zealand Māori) and Western (Samoa, Tonga, Niue, Tokelau, Tuvalu, Rotuma) Polynesian genomes and those of other Pacifi c populations. 24 These differences include variants at either lower or higher frequencies than observed elsewhere, together with novel variations that are not present at all in large catalogues of genomic variation derived from other populations (TM, SR unpublished). ...
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Precision medicine seeks to draw on data from both individuals and populations across disparate domains to influence and support diagnosis, management and prevention in healthcare at the level of the individual patient and their family/whānau. Central to this initiative is incorporating the effects of the inherent variation that lies within genomes and can influence health outcomes. Identifying and interpreting such variation requires an accurate, valid and representative dataset to firstly define what variants are present and then assess the potential relevance for the health of a person, their family/whānau and the wider community to which they belong. Globally the variation embedded within genomes differs enormously and has been shaped by the size, constitution, historical origins and evolutionary history of their source populations. Māori, and more broadly Pacific peoples, differ substantially in terms of genomic variation compared to the more closely studied European and Asian populations. In the absence of accurate genomic information from Māori and Pacific populations, the precise interpretation of genomic data and the success and benefits of genomic medicine will be disproportionately less for those Māori and Pacific peoples. In this viewpoint article we, as a group of healthcare professionals, researchers and scientists, present a case for assembling genomic resources that catalogue the characteristics of the genomes of New Zealanders, with an emphasis on peoples of Māori and Polynesian ancestry, as a healthcare imperative. In proposing the creation of these resources, we note that their governance and management must be led by iwi and Māori and Pacific representatives. Assembling a genomic resource must be informed by cultural concepts and values most especially understanding that, at a physical and spiritual level, whakapapa is embodied within the DNA of a person. Therefore DNA and genomic data that connects to whakapapa (genealogy) is considered a taonga (something precious and significant), and its storage, utilisation and interpretation is a culturally significant activity. Furthermore, such resources are not proposed to primarily enable comparisons between those with Māori and broader Pacific ancestries and other Aotearoa peoples but to place an understanding of the genetic contributors to their health outcomes in a valid context. Ongoing oversight and governance of such taonga by Māori and Pacific representatives will maximise hauora (health) while also minimising the risk of misuse of this information.
... Recent studies of other taxa have demonstrated that short fragments of the mitogenome, and particularly, conserved regions like Cyt B, do not generally provide sufficient data to fully characterise the genetic variation within a population or even a species (Benton et al., 2012; Duggan et al., 2014;Greig et al., 2015;Knapp et al., 2012b;Llamas et al., 2016). With the advancement of DNA sequencing technologies such as NGS and targeted DNA enrichment methodologies, retrieving complete mitogenome and even nuclear genome sequences from ancient samples is now more feasible (Llamas et al., 2016;Millar et al., 2008;Reich et al., 2010;Sankararaman et al., 2016). ...
... While aDNA studies have traditionally focused on short, informative regions, such as the HVR, recent improvements to sequencing techniques allow researchers to sequence complete mitochondrial genomes from degraded, ancient samples (Carpenter et al., 2013;Dabney et al., 2013a;Green et al., 2008;Greig et al., 2015;Heupink et al., 2016;Knapp et al., 2012b;Llamas et al., 2016;Maricic et al., 2010;Matisoo-Smith et al., 2016;Sankararaman et al., 2016). Using NGS methods, identifying differences due to DNA damage or contamination is more feasible and recent studies have demonstrated that complete mitogenomes provide better resolution for phylogenetic analyses than short fragments such as the HVR (Benton et al., 2012;Duggan et al., 2014;Greig et al., 2015;Knapp et al., 2012b;Llamas et al., 2016). Kimura et al. (2016) analysed short fragments of the HVR (79 bp) and the Cyt B region (concatenated 288 bp) and found little variation within the HVR, though a surprising level of variation in the Cyt B region, particularly for the Grand Bay sample. ...
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The domestic guinea pig (Cavia porcellus) was translocated from South America to several Caribbean islands sometime after 500 CE. Identifying the timing and routes of guinea pig translocation can provide a proxy for human interaction in the region. A recent investigation of aDNA of Caribbean guinea pig remains, based on sequences from short regions of the mitochondrial D-loop and cytochrome B regions, suggested a Colombian origin and single introduction of guinea pigs to the Caribbean. Here, we present the first complete mitogenome sequences for three ancient guinea pigs from Puerto Rico, Antigua and Carriacou, as well as for a modern Puerto Rican specimen, which allow us to clarify and expand upon the results of the earlier study. Complete mitogenome sequences indicate that there are at least two different mitochondrial DNA haplotypes in the ancient Caribbean guinea pigs, suggesting two distinct ancient introductions and a modern reintroduction of guinea pigs to Puerto Rico. Our results demonstrate the value of Next Generation Sequencing and the analysis of complete mitogenome sequences to investigate genetic variation and translocation of guinea pigs into the Caribbean.
... In this study, we examined the maternal population structure and the history of admixture across Oceania. Previous studies exploring the maternal histories of the area have been limited because they largely make use of only a small portion of the genome known as the hypervariable region (HVR) (e.g., see Kayser et al., 24 Friedlaender et al., 25 Delfin et al. 41 ); other studies making use of whole mtDNA sequences from Oceania have been limited in terms of sample sizes and number of populations analyzed (e.g., see Soares et al., 42 Benton et al. 43 ). Our data set is, to our knowledge, the most comprehensive to date, and consists of 1,331 whole mitochondrial genome sequences from 34 populations spread from the Bismarck Archipelago to Polynesia (Figure 1). ...
... 31 Haplogroups were assigned to consensus sequences for each sample with the Haplogrep webtool and Phylotree Build 15. 60,61 The haplogroup assigned to each individual is provided in Table S1, and haplogroup frequencies for each population are in Table S2. The relative frequencies of haplogroups of putative Near Oceanian, Austronesian (haplogroup B and sublineages), or other origin are depicted in Figure 2. In general, the frequencies of haplogroups of putative Near Oceanic origin are greater in New Britain and Bougainville and then decrease in frequency the further out a population is in the Pacific Santa Cruz (47) Anem (32) Ata (28) Nakanai (42) Nagovisi (38) Siwai (26) Buka (11) Torau (34) Nasioi (41) Buin (29) Simbo (22) Russell (39) Kolombangara (18) Makira (17) Isabel (52) Savo (40) Vella Lavella (51) Guadalcanal (50) Choiseul (33) Gela (40) Malaita (89) Ranongga (47) Shortlands (14) Niue (21) Cook Islands (65) Tuvalu (50) Futuna (48) Samoa (47) Tonga (52) Fiji (49) Bellona (38) Rennell (43) Ontong Java (32) Tikopia (46) Relative haplogroup frequency Near Oceanian B Other Table S2. ...
... The general frequency of the backmutation in haplogroup B4a1a1a1 remains constant at approximately 20% and was found in all groups except Santa Cruz and the three populations from New Britain (Table S2); the latter result probably reflects the low frequency of haplogroup B4a1a1a1 in these populations. In addition, haplogroup B4a1a1a3, identified previously as a Maori-specific haplogroup, 43 is present in additional samples from Remote Oceania, reaching a frequency of 14% in the Cook Islands (Table S2). ...
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A widely accepted two-wave scenario of human settlement of Oceania involves the first out-of-Africa migration ca 50,000 ya, and one of the most geographically-widespread dispersals of people, known as the Austronesian expansion, which reached the Bismarck Archipelago by about 3,450 ya. While earlier genetic studies provided evidence for extensive sex-biased admixture between the incoming and the indigenous populations, some archaeological, linguistic and genetic evidence indicates a more complicated picture of settlement. To study regional variation in Oceania in more detail, we have compiled a genome-wide dataset of 823 individuals from 72 populations (including 50 populations from Oceania) and over 620,000 autosomal SNPs. We show that the initial dispersal of people from the Bismarck Archipelago into Remote Oceania occurred in a "leapfrog" fashion, completely by-passing the main chain of the Solomon Islands, and that the colonization of the Solomon Islands proceeded in a bi-directional manner. Our results also support a divergence between western and eastern Solomons, in agreement with the sharp linguistic divide known as the Tryon-Hackman line. We also report substantial post-Austronesian gene flow across the Solomons. In particular, Santa Cruz (in Remote Oceania) exhibits extraordinarily high levels of Papuan ancestry that cannot be explained by a simple bottleneck/founder event scenario. Finally, we use simulations to show that discrepancies between different methods for dating admixture likely reflect different sensitivities of the methods to multiple admixture events from the same (or similar) sources. Overall, this study points to the importance of fine-scale sampling to understand the complexities of human population history.
... Genetic diversity in Polynesia is also likely to have been further reduced by disease epidemics introduced by early European explorers and colonists, as well as the spread of these diseases in more recent history (e.g., 1918 Influenza epidemic) (Kirch and Rallu 2007). As a result, the few studies that have measured modern genetic diversity in East Polynesia found limited genetic variation (Benton et al. 2012;Murray-McIntosh et al. 1998;Whyte et al. 2005). It is possible, however, that future studies examining larger amounts of nuclear DNA through SNP (Single-Nucleotide-Polymorphism) panels or whole genome sequencing may provide greater resolution. ...
Article
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Ancient human migrations provide the critical genetic background to historical and contemporary human demographic patterns. However, our ability to infer past human migration events, especially those that occurred over rapid timescales, is often limited. A key example is the peopling of Polynesia, where the timing is relatively well defined, but the exact routes taken during the final stages and the source populations are not. Here, we discuss the technical limitations of current methods for inferring rapid human migration events, using the final stages of Polynesian migration as an example. We also introduce a promising new proxy method to infer human migrations-patterns of bacterial evolution within ancient dental calculus (calcified plaque). While we focus on Polynesia, this method should be applicable to other past migrations, enhancing our understanding of human prehistory and revealing the crucial events that shaped it.
... The resolution of mtDNA on all four sequences is sufficient to say they were members of the B4a1a1 group, the common clade of mtDNA across Marginal Eastern Polynesia. The two individuals with high DNA quality results included B4a1a1a3 and B4a1a1a, and two out of three mutations reported to be unique to modern M? aori were found [89]. With such a small sample size it is difficult to interpret these beyond the generalization that some of the mtDNA sequences currently only found in M? aori may have their origins either early in the settlement of New Zealand or perhaps in Central Eastern Polynesia in the generations immediately prior. ...
... The resolution of mtDNA on all four sequences is sufficient to say they were members of the B4a1a1 group, the common clade of mtDNA across Marginal Eastern Polynesia. The two individuals with high DNA quality results included B4a1a1a3 and B4a1a1a, and two out of three mutations reported to be unique to modern M?ori were found [89]. With such a small sample size it is difficult to interpret these beyond the generalization that some of the mtDNA sequences currently only found in M?ori may have their origins either early in the settlement of New Zealand or perhaps in Central Eastern Polynesia in the generations immediately prior. ...
Article
Full-text available
Integration of archaeology, modern genetics, and ancient DNA holds promise for the reconstruction of the human past. We examine the advances in research on the indigenous peoples of Polynesia to determine: (1) what do archaeological and genetic data (ancient and modern DNA) tell us about the origins of Polynesians; and, (2) what evidence is there for long-distance travel and contacts between Polynesians and indigenous populations of the Americas? We note that the general dispersal pattern of founding human populations in the remote islands of the Pacific and long-distance interaction spheres continue to reflect well-established models. New research suggests that the formation of an Ancestral Polynesia Culture in Western Polynesia may have involved differential patterns of dispersal followed by significant later migrations. It has also been suggested that the pause between the settlement of Western and Eastern Polynesia was centuries longer than currently thought, followed by a remarkably rapid pulse of island colonization. Long-distance travel between islands of the Pacific is currently best documented through the sourcing of artifacts, while the discovery of admixture of Native American DNA within the genome of the people from Easter Island (Rapa Nui) is strong new evidence for sustained contacts between Polynesia and the Americas.
... They identified eight mtDNA lineages (again, based on sequencing the HVR) in Maori and estimated the founding female population was approximately 190 women. Recently, with both the developments in technology and more general acceptance of genetic ancestry studies, more data for New Zealand Maori and other East Polynesian populations has begun to accumulate (Benton et al. 2012(Benton et al. , 2015Kim et al. 2012) including ancient DNA data (Deguilloux et al. 2011;Knapp et al. 2012). Since 2013 we have collected and sequenced over 2000 complete mitochondrial genomes from the New Zealand population generally, which included nearly 200 individuals of Maori and Polynesian maternal ancestry (Matisoo-Smith lab unpublished data). ...
... The data on complete mitogenomes for East Polynesians indicates a number of new lineages within the B4a1a1 haplogroup. Benton, in a study of 20 non-related individuals from one iwi (tribal group) on the East Coast of the North Island, identified six new variants resulting in three new haplogroups (Benton et al. 2012). These three were initially identified by Benton et al. as being Maori specific, yet we have found these in our (unpublished) data and other samples (Duggan et al. 2014;Kim et al. 2012) from other East and Central Polynesian populations. ...
Chapter
The settlement of the Polynesian Triangle, culminating with the settlement of Aotearoa/New Zealand within the last 750 years, represents the last major migration event of humans as they dispersed across the globe. Despite this relatively short human history in the region, humans have had a significant impact on the island environments they inhabited. Reconstructing the process of Polynesian settlement, including population origins, the timing of arrival and size of colonising populations as well as those of the animals they introduced, will not only allow us to better understand the true impact of human arrival in Aotearoa, but help us appreciate the broader impact of humans on the environment and of the environment on humans. Both ancient and modern DNA studies of humans and the plants and animals they introduced to the island environments they settled can help us to reconstruct these population histories and therefore better address these important questions. Similarly, ancient DNA analyses of the remains of native fauna can provide key information regarding the true impacts of human arrival in island ecosystems.