Mitochondrial DNA variability of West New Guinea populations.

This paper reports human mitochondrial DNA variability in West New Guinea (the least known, western side of the island of New Guinea), not yet described from a molecular perspective. The study was carried out on 202 subjects from 12 ethnic groups, belonging to six different Papuan language families, representative of both mountain and coastal plain areas. Mitochondrial DNA hypervariable region 1 (HVS 1) and the presence of the 9-bp deletion (intergenic region COII-tRNA(Lys)) were investigated. HVS 1 sequencing identified 73 polymorphic sites defining 89 haplotypes; the 9-bp deletion, which is considered a marker of Austronesian migration in the Pacific, was found to be absent in the whole West New Guinea study sample. Statistical analysis applied to the resulting haplotypes reveal high heterogeneity and an intersecting distribution of genetic variability in these populations, despite their cultural and geographic diversity. The results of subsequent phylogenetic approaches subdivide mtDNA diversity in West New Guinea into three main clusters (groups I-III), defined by sets of polymorphisms which are also shared by some individuals from Papua New Guinea. Comparisons with worldwide HVS 1 sequences stored in the MitBASE database show the absence of these patterns outside Oceania and a few Indonesian subjects, who also lack the 9-bp deletion. This finding, which is consistent with the effects of genetic drift and prolonged isolation of West New Guinea populations, lead us to regard these patterns as New Guinea population markers, which may harbor the genetic memory of the earliest human migrations to the island.     

Patterns of Y-chromosome diversity intersect with the Trans-New Guinea hypothesis

The island of New Guinea received part of the first human expansion out of Africa (>40,000 years ago), but its human genetic history remains poorly understood. In this study, we examined Y-chromosome diversity in 162 samples from the Bird's Head region of northwest New Guinea (NWNG) and compared the results with previously obtained data from other parts of the island. NWNG harbors a high level of cultural and linguistic diversity and is inhabited by non-Austronesian (i.e., Papuan)-speaking groups as well as harboring most of West New Guinea's (WNG) Austronesian-speaking groups. However, 97.5% of its Y-chromosomes belong to 5 haplogroups that originated in Melanesia; hence, the Y-chromosome diversity of NWNG (and, according to available data, of New Guinea as a whole) essentially reflects a local history. The remaining 2.5% belong to 2 haplogroups (O-M119 and O-M122) of East Asian origin, which were brought to New Guinea by Austronesian-speaking migrants around 3,500 years ago. Thus, the Austronesian expansion had only a small impact on shaping Y-chromosome diversity in NWNG, although the linguistic impact of this expansion to this region was much higher. In contrast, the expansion of Trans-New Guinea (TNG) speakers (non-Austronesian) starting about 6,000-10,000 years ago from the central highlands of what is now Papua New Guinea, presumably in combination with the expansion of agriculture, played a more important role in determining the Y-chromosome diversity of New Guinea. In particular, we identified 2 haplogroups (M-P34 and K-M254) as suggestive markers for the TNG expansion, whereas 2 other haplogroups (C-M38 and K-M9) most likely reflect the earlier local Y-chromosome diversity. We propose that sex-biased differences in the social structure and cultural heritage of the people involved in the Austronesian and the TNG expansions played an important role (among other factors) in shaping the New Guinean Y-chromosome landscape.     

Biogeographic models of gene flow in two waterfowl of the Australo‐Papuan tropics

There are many large, easy‐to‐observe anseriform birds (ducks, geese, and swans) in northern Australia and New Guinea and they often gather in large numbers. Yet, the structure of their populations and their regional movements are poorly understood. Lack of understanding of population structure limits our capacity to understand source‐sink dynamics relevant to their conservation or assess risks associated with avian‐borne pathogens, in particular, avian influenza for which waterfowl are the main reservoir species. We set out to assess present‐day genetic connectivity between populations of two widely distributed waterfowl in the Australo‐Papuan tropics, magpie goose Anseranas semipalmata (Latham, 1798) and wandering whistling‐duck Dendrocygna arcuata (Horsfield, 1824). Microsatellite data were obtained from 237 magpie geese and 64 wandering whistling‐duck. Samples were collected across northern Australia, and at one site each in New Guinea and Timor Leste. In the wandering whistling‐duck, genetic diversity was significantly apportioned by region and sampling location. For this species, the best model of population structure was New Guinea as the source population for all other populations. One remarkable result for this species was genetic separation of two flocks sampled contemporaneously on Cape York Peninsula only a few kilometers apart. In contrast, evidence for population structure was much weaker in the magpie goose, and Cape York as the source population provided the best fit to the observed structure. The fine scale genetic structure observed in wandering whistling‐duck and magpie goose is consistent with earlier suggestions that the west‐coast of Cape York Peninsula is a flyway for Australo‐Papuan anseriforms between Australia and New Guinea across Torres Strait.     

Altitude,language, and class I HLA allele frequencies in Papua New Guinea

Class I HLA gene frequencies show considerable variation over short geographical distances in Papua New Guinea. Hypotheses to account for this invoke natural selection, population structure, the pattern of population movement, or past demographic changes. To determine the role of the various factors in shaping this distribution, we have studied correlations between HLA-based genetic distances, geographical distances, altitude, and linguistic differences in Papua New Guinea. Linguistic differences at the family or stock level within the Trans-New Guinea Phylum generally correspond to genetic differences. However, on the basis of their HLA gene frequencies, speakers of Austronesian (AN) languages do not form a distinct group of populations. Linguistic variation and spatial autocorrelation do not fully account for the altitudinal cline differences noted in gene frequencies, particularly at the HLA-A locus. We propose that the distribution of HLA gene frequencies in Papua New Guinea is partially under the control of selection operating differentially along the altitude gradient. © 1994 Wiley-Liss, Inc.     

Genetic variability,local selection and demographic history: genomic evidence of evolving towards allopatric speciation in Asian seabass

Genomewide analysis of genetic divergence is critically important in understanding the genetic processes of allopatric speciation. We sequenced RAD tags of 131 Asian seabass individuals of six populations from South‐East Asia and Australia/Papua New Guinea. Using 32 433 SNPs, we examined the genetic diversity and patterns of population differentiation across all the populations. We found significant evidence of genetic heterogeneity between South‐East Asian and Australian/Papua New Guinean populations. The Australian/Papua New Guinean populations showed a rather lower level of genetic diversity. F_ST and principal components analysis revealed striking divergence between South‐East Asian and Australian/Papua New Guinean populations. Interestingly, no evidence of contemporary gene flow was observed. The demographic history was further tested based on the folded joint site frequency spectrum. The scenario of ancient migration with historical population size changes was suggested to be the best fit model to explain the genetic divergence of Asian seabass between South‐East Asia and Australia/Papua New Guinea. This scenario also revealed that Australian/Papua New Guinean populations were founded by ancestors from South‐East Asia during mid‐Pleistocene and were completely isolated from the ancestral population after the last glacial retreat. We also detected footprints of local selection, which might be related to differential ecological adaptation. The ancient gene flow was examined and deemed likely insufficient to counteract the genetic differentiation caused by genetic drift. The observed genomic pattern of divergence conflicted with the ‘genomic islands’ scenario. Altogether, Asian seabass have likely been evolving towards allopatric speciation since the split from the ancestral population during mid‐Pleistocene.     

A multivariate approach to fingerprint variation in Papua New Guinea: Implications for prehistory

Fingerprint data from three Markham Valley populations of Papua New Guinea are presented. Initial comparisons with data from elsewhere in New Guinea by conventional bivariate methods suggest hypotheses regarding prehistory, but these methods are inconclusive. Because of this shortcoming, the application of discriminant analysis to dermatoglyphic data is justified and cautiously demonstrated. Discriminant analysis is a valid approach to the parsimonious study of fingerprint relationships among human populations. Significant discriminating variables are then used with the limited published data to display historical relationships. These marker traits include the separate frequencies of thumb, middle fingers, and little finger patterning, and the complexity of the thenar eminence. With regard to prehistory, it is concluded that fingerprint data support the hypothesis of separate origins and migrations for Papuan- and Melanesian-speaking peoples. Furthermore, it is suggested that these data support the linguistic hypothesis of a second Papuan migration of Trans New Guinea Phylum speakers, up the Markham Valley into the New Guinea Highlands. Finally, gene flow is indicated from Melanesian speakers of the north coast into the interior through the Sepik and Ramu River valleys, affecting both the Trans New Guinea Phylum and other unrelated Papuan groups. Moreover, there are numerous suggestions of recent reciprocal genetic exchange between neighboring Melanesians and Papuans, without obliterating the older, separate origins of these peoples. These results suggest that fingerprints have greater phylogenetic stability than other biological parameters used in the past.     

A microsatellite study to disentangle the ambiguity of linguistic,geographic, ethnic and genetic influences on tribes of India to get a better clarity of the antiquity and peopling of South Asia

An understanding of the genetic affinity and the past history of the tribal populations of India requires the untangling of the confounding influences of language, ethnicity, and geography on the extant diverse tribes. The present study examines the genetic relationship of linguistically (Dravidian, Austro‐Asiatic, and Tibeto‐Burman) and ethnically (Australian and East Asian) diverse tribal populations (46) inhabiting different regions of the Indian subcontinent. For the purpose, we have utilized the published data on allele frequency of 15 autosomal STR loci of our study on six Adi sub‐tribes of Arunachal Pradesh and compared the same with the reported allele frequency data, for nine common autosomal STR loci, of 40 other tribes. Phylogenetic and principal component analyses exhibit geography based clustering of Tibeto‐Burman speakers and separation of the Mundari and Mon‐Khmer speaking Austro‐Asiatic populations. The combined analyses of all 46 populations show clustering of the groups belonging to same ethnicity and inhabiting contiguous geographic regions, irrespective of their different languages. These results help us to reconstruct and understand three plausible scenarios of the antiquity of Indian tribal populations: the Dravidian and Austro‐Asiatic (Mundari) tribes were possibly derived from common early settlers; the Tibeto‐Burman tribes possibly belonged to a different ancestry and the Mon‐Khmer speaking Austro‐Asiatic populations share a common ancestry with some of the Tibeto‐Burman speakers. Am J Phys Anthropol, 2009. © 2009 Wiley‐Liss, Inc.     

Genetic distance: probing the origin of a Papua New Guinea isolate

In an attempt to elucidate the origin of an isolated peripheral Highland, Papua New Guinea population (the Karimui), HLA, blood group and serum protein markers were investigated. Due to the paucity of published HLA marker data, genetic distances using non-HLA markers were constructed between populations surrounding the Karimui and compared in 3-dimensions by multidimensional scaling analysis. Genetically, the Karimui is most closely associated with Highland populations to the east and northeast. In a attempt to develop a more global view of relationships, distances constructed from HLA marker data between 2 close Highland populations, 2 Coastal Papua New Guinea populations and 4 Australian aborigine populations were compared. The Karimui associated most closely with the Highland populations and equidistantly and at opposite poles from both the Coastal Papuan and aborigine populations. A paradigm of the composition of the founder group and the early population dynamics is developed from genetic, linguistic and anthropologic data.     

Blood group, red cell enzyme and serum protein types in the Buka Islanders, Papua New Guinea

Genetic marker studies on a sample of 80 speakers of the Petats and Tinputs families of languages, all pupils at a single high school, indicate a homogeneity among them which can be extrapolated to their areas of origin. Buka and its offshore islands and the northern part of Bougainville Island in the North Solomons Province of Papua New Guinea. Several markers systems, most notably first-locus phosphoglucomutase and liver acetyltransferase, reinforce the morphological evidence that these peoples are quite distinct from most other Papua New Guinea populations, with whom, however, there has been some gene exchange, probably through East New Britain. Their principal affinities are with the peoples of the Solomon Islands to the south.     

Contrasting phylogeographic signatures in two Australo‐Papuan bowerbird species complexes (Aves: Ailuroedus)

The Australo‐Papuan catbird genus Ailuroedus has a complex distribution and a contested taxonomy. Here, we integrate phylogenetic analysis of DNA data and morphology to study the group's biogeography and to re‐examine its taxonomy. We couple phylogeographic and abiotic data to examine differences between the major groups defined in our phylogenetic analysis. Our results are consistent with Ailuroedus catbirds being divided into two species complexes, one distributed in humid forests in the lowlands on New Guinea and another in comparably drier and colder forests mainly in mid‐mountains on New Guinea and Australia. Vicariant events during the Pliocene are surmised to have been the major force in shaping the contemporary phylogeographical signature of this genus. Several previously suggested vicariant events, such as fragmentation of xeric forests in Australia and the uplift of the central mountain range on New Guinea, are reinforced as important Pliocene barriers for tropical forest taxa in this region. Interaction between Pleistocene climatic fluctuations and differences in habitat requirements may explain a higher and more recent population structures in the mid‐mountain catbird complex and the lack of representatives from the lowland clade in the comparably drier Australia. Phylogeographical patterns in both catbird complexes, respectively, both comply and deviate from other lowland and mid‐mountain taxa in the region. This highlights that taxon‐specific properties, such as their historical spatial and ecological distributions, capacity to disperse and tolerance to habitat changes, affect the phylogeographical histories of organisms. Within both species complexes, the genetic differentiation between several geographically isolated populations was found to exceed those commonly observed for avian sister species. As these genetically distinct taxa also were found to be morphological diagnosable, we suggest a revised classification of the genus Ailuroedus, where we recognize three species within the lowland complex and seven species within the mid‐mountain complex.     

Comparative population genetics of mimetic Heliconius butterflies in an endangered habitat; Brazil's Atlantic Forest

Background

The islands of North Maluku, Indonesia occupy a central position in the major prehistoric dispersal streams that shaped the peoples of Island Southeast Asia and the Pacific. Within this region a linguistic contact zone exists where speakers of Papuan and Austronesian languages reside in close proximity. Here we use population genetic data to assess the extent to which North Maluku populations experienced admixture of Asian genetic material, and whether linguistic boundaries reflect genetic differentiation today.

Results

Autosomal and X-linked markers reveal overall Asian admixture of 67% in North Maluku, demonstrating a substantial contribution of genetic material into the region from Asia. We observe no evidence of population structure associated with ethnicity or language affiliation.

Conclusions

Our data support a model of widespread Asian admixture in North Maluku, likely mediated by the expansion of Austronesian-speaking peoples into the region during the mid Holocene. In North Maluku there is no genetic differentiation in terms of Austronesian- versus Papuan-speakers, suggesting extensive gene flow across linguistic boundaries. In a regional context, our results illuminate a major genetic divide at the Molucca Sea, between the islands of Sulawesi and North Maluku. West of this divide, populations exhibit predominantly Asian ancestry, with very little contribution of Papuan genetic material. East of the Molucca Sea, populations show diminished rates of Asian admixture and substantial persistence of Papuan genetic diversity.     

Connectivity and the development of population genetic structure in Indo‐West Pacific coral reef communities

Aim To identify connectivity patterns among coral reefs of the Indo‐West Pacific. Projecting connectivity forward in time provides a framework for studying long‐term source–sink dynamics in the region, and makes it possible to evaluate the manner in which migration shapes population genetic structure at regional scales. This information is essential for addressing critical gaps in knowledge for conservation planning efforts in one of the most biologically diverse regions on earth. Location Coral reefs of the Indo‐West Pacific, ranging from 15° S to 30° N and 95° E to 140° E. Methods Individual‐based biophysical dispersal models were used in conjunction with matrix projection to identify the expected patterns of exchange between coral reefs over time. Results Present‐day oceanographic conditions lead to the transport of larvae from the South China Sea into the Coral Triangle region via the Sulu Sea, and from northern Papua New Guinea and the Solomon Islands via Halmahera. The directionality of the system leads to the expected accumulation of organisms from outlying areas into the Coral Triangle region over time, particularly in the vicinity of the Maluku Islands and eastern Sulawesi. Coral reefs in Papua New Guinea, the Sulu Archipelago and areas within the Philippines are expected to be areas of high diversity as well. Main conclusions Biophysical dispersal models, used in conjunction with matrix projection, provide an effective means of simulating connectivity structure across the Indo‐West Pacific and thereby evaluating the directionality of genetic diversity. Migration appears to have a significant influence on population genetic structure in the region. Based on present‐day ocean currents, coral reefs in the South China Sea, northern Papua New Guinea and the Solomon Islands are contributing to high levels of diversity in the Coral Triangle.     

Evolutionary origins of taro (Colocasia esculenta) in Southeast Asia

As an ancient clonal root and leaf crop, taro (Colocasia esculenta, Araceae) is highly polymorphic with uncertain genetic and geographic origins. We explored chloroplast DNA diversity in cultivated and wild taros, and closely related wild taxa, and found cultivated taro to be polyphyletic, with tropical and temperate clades that appear to originate in Southeast Asia sensu lato. A third clade was found exclusively in wild populations from Southeast Asia to Australia and Papua New Guinea. Our findings do not support the hypothesis of taro domestication in Papua New Guinea, despite archaeological evidence for early use or cultivation there, and the presence of apparently natural wild populations in the region (Australia and Papua New Guinea).     

Red cell antigen, serum protein and red cell enzyme polymorphisms in Eastern Highlanders of New Guinea

A series of 1,187 blood samples from eight population groups in the Eastern Highlands of Papua New Guinea were tested for genetic variation in blood groups, serum proteins and red cell enzyme systems. The populations belonged to the language groups Gahuku-Asarc-Bena Bena, Kamano, Yagaria, Keiagana, Fore, Agarabe, Auyana and Tairora. Polymorphic variation was found in the ABO, MNS, P1, Rh, Hp, Tf, SEP, 6-PGD, ADA, MDH, and PGM genetic systems. East to West variation was shown in the language groups; the O, S, R2, and R0 genes increase in frequency from East to West and the A, R1, and M genes decrease in the same direction. In the East higher frequencies were found for the Du antigen, for the PGM21 gene and for a PGM second locus variant. The MDH 3 variant was found in all the populations, its highest value being in the Tairora.     

A 9.1-kb insertion/deletion polymorphism suggests a common pattern of genetic diversity in Island Melanesia

Earlier reports suggest a distinct pattern of genetic variation linked to both language and geographic distance in Island Melanesia. Inland Papuan-speaking populations from different islands tend to share one allelic profile, while shore-based or more cosmopolitan populations share another, related to Southeast Asian influence over the past 3000 years. In the present paper, we report the genotypes and allele frequencies of an informative 9.1-thousand-base-pairs (kb) insertion/deletion polymorphism in 19 populations living in Island Melanesia. The populations studied inhabit the islands of New Britain, New Ireland, New Hanover, and Mussau in the Bismarck Archipelago, and speak either Austronesian or Papuan languages. We also include for reference a collection from New Guinea and Bougainville. The data show a marked fluctuation in the allele frequency among the different isolates, with the 9.1-kb(-) allele frequency ranging from 0.67 to 0.98. The deletion allele reaches fixation in some Papuan-speaking interior populations of New Britain, as well as in the interiors of New Guinea and Bougainville. However, certain inland Austronesian-speaking populations also share a similar high frequency of the deletion. Our data suggest that language distinctions are generally, but not invariably, indicative of diverse allelic patterns in this complex region, where inland groups on large islands tend to be often distinctive from shore-based populations.     

Population genetics of Anopheles koliensis through Papua New Guinea: New cryptic species and landscape topography effects on genetic connectivity

New Guinea is a topographically and biogeographically complex region that supports unique endemic fauna. Studies describing the population connectivity of species through this region are scarce. We present a population and landscape genetic study on the endemic malaria‐transmitting mosquito, Anopheles koliensis (Owen). Using mitochondrial and nuclear sequence data, as well as microsatellites, we show the evidence of geographically discrete population structure within Papua New Guinea (PNG). We also confirm the existence of three rDNA ITS2 genotypes within this mosquito and assess reproductive isolation between individuals carrying different genotypes. Microsatellites reveal the clearest population structure and show four clear population units. Microsatellite markers also reveal probable reproductive isolation between sympatric populations in northern PNG with different ITS2 genotypes, suggesting that these populations may represent distinct cryptic species. Excluding individuals belonging to the newly identified putative cryptic species (ITS2 genotype 3), we modeled the genetic differences between A. koliensis populations through PNG as a function of terrain and find that dispersal is most likely along routes with low topographic relief. Overall, these results show that A. koliensis is made up of geographically and genetically discrete populations in Papua New Guinea with landscape topography being important in restricting dispersal.     

Three new species of Oreophryne (Anura,Microhylidae) from Papua New Guinea

I describe three new species of the diverse microhylid frog genus Oreophryne from Papua New Guinea. Two of these occur in two isolated mountain ranges along the northern coast of Papua New Guinea; the third is from Rossel Island in the very southeasternmost part of the country. All three are the first Oreophryne known from these areas to have a cartilaginous connection between the procoracoid and scapula, a feature usually seen in species far to the west or from the central cordillera of New Guinea. Each of the new species also differs from the many other Papuan Oreophryne in a variety of other morphological, color-pattern, and call features. Advertisement-call data for Oreophryne species from the north-coast region suggest that they represent only two of the several call types seen in regions further south, consistent with the relatively recent derivation of these northern regions as accreted island-arc systems. The distinctively different, whinnying, call type of the new species from Rossel Island occurs among other Oreophryne from southeastern Papua New Guinea but has been unreported elsewhere, raising the possibility that it may characterize a clade endemic to that region.     

Gene flow and natural selection in oceanic human populations inferred from genome-wide SNP typing

It is suggested that the major prehistoric human colonizations of Oceania occurred twice, namely, about 50,000 and 4,000 years ago. The first settlers are considered as ancestors of indigenous people in New Guinea and Australia. The second settlers are Austronesian-speaking people who dispersed by voyaging in the Pacific Ocean. In this study, we performed genome-wide single-nucleotide polymorphism (SNP) typing on an indigenous Melanesian (Papuan) population, Gidra, and a Polynesian population, Tongans, by using the Affymetrix 500K assay. The SNP data were analyzed together with the data of the HapMap samples provided by Affymetrix. In agreement with previous studies, our phylogenetic analysis indicated that indigenous Melanesians are genetically closer to Asians than to Africans and European Americans. Population structure analyses revealed that the Tongan population is genetically originated from Asians at 70% and indigenous Melanesians at 30%, which thus supports the so-called Slow train model. We also applied the SNP data to genome-wide scans for positive selection by examining haplotypic variation and identified many candidates of locally selected genes. Providing a clue to understand human adaptation to environments, our approach based on evolutionary genetics must contribute to revealing unknown gene functions as well as functional differences between alleles. Conversely, this approach can also shed some light onto the invisible phenotypic differences between populations.     

Human Genetics, Paleoenvironments, and Malaria: Relationships and Implications for the Settlement of Oceania

Lapita is a distinctive ceramic style that first appeared in the Bismarck Archipelago about 3600 B.P. and over the next few centuries spread throughout island Melanesia. For many prehistorians the distribution of Lapita sherds identifies the expansion of Austronesian-speaking populations through Oceania. This article addresses the Lapita language question by exploring the implications of the relationship among gamma globulin (Gm) genetics, paleoenvironments, malaria, natural selection, and prehistoric settlement patterns. Archeological sites with Lapita ceramics are consistently located in coastal lowlands, which in some parts of Oceania would have been malarious areas. Drawing on recent evidence that Austronesian-speaking populations in Near Oceania possess a genetic advantage over Non-Austronesian speakers with regard to malaria, we contend that Austronesian speakers have been able to occupy—on a permanent basis—malarious coastal lowlands that were detrimental to Non-Austronesian speakers. It follows, therefore, that the inhabitants of those Lapita sites spoke one or more of the Austronesian languages.     

Immunogenetic studies of two recently contacted populations from Papua New Guinea

We have examined the HLA profiles of the Hagahai and the Haruai people, two linguistic groups in the remote western Schrader mountains who have only recently had administrative contact, and compared them with those of other populations in Papua New Guinea. None of the antigens detected in the two groups was found missing in other populations although significant differences in allele frequencies exist. Recent contact history does not appear to have played any significant role in shaping these differences. Similarly, no evidence of differential selection pressures contributing to HLA heterogeneity was found. The genetic profiles of the Hagahai and the Haruai appear to be a result of recent admixture between unrelated, genetically disparate groups.