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Ricaut et al. / Forensic Science International 151 (2005) 31-35 ...doi:10.1016/j.forsciint.2004.07.001 pmid:15935940 fatcat:wwsyijpcmbdfvfyt2rbv2dppju
Resources: Matthew Leavesley, Mayukh Mondal, François-Xavier Ricaut. Supervision: Nicolas Brucato, Mayukh Mondal, François-Xavier Ricaut. Validation: Nicolas Brucato, Mayukh Mondal. ... Investigation: Nicolas Brucato, Jason Kariwiga, John Muke, Matthew Leavesley, François-Xavier Ricaut. administration: Nicolas Brucato, Matthew Leavesley, Mayukh Mondal, François-Xavier Ricaut. ...doi:10.1371/journal.pone.0253921 pmid:34288918 fatcat:pyikdpbu45ealhpeixdkakd6pe
New Guineans represent one of the oldest locally continuous populations outside Africa, harboring among the greatest linguistic and genetic diversity on the planet. Archeological and genetic evidence suggest that their ancestors reached Sahul (present day New Guinea and Australia) by at least 55,000 years ago (kya). However, little is known about this early settlement phase or subsequent dispersal and population structuring over the subsequent period of time. Here we report 379 complete Papuandoi:10.1038/s10038-020-0781-3 pmid:32483274 fatcat:oav5cgb3nrcx5l7eog47toaepe
more »... itochondrial genomes from across Papua New Guinea, which allow us to reconstruct the phylogenetic and phylogeographic history of northern Sahul. Our results support the arrival of two groups of settlers in Sahul within the same broad time window (50-65 kya), each carrying a different set of maternal lineages and settling Northern and Southern Sahul separately. Strong geographic structure in northern Sahul remains visible today, indicating limited dispersal over time despite major climatic, cultural, and historical changes. However, following a period of isolation lasting nearly 20 ky after initial settlement, environmental changes postdating the Last Glacial Maximum stimulated diversification of mtDNA lineages and greater interactions within and beyond Northern Sahul, to Southern Sahul, Wallacea and beyond. Later, in the Holocene, populations from New Guinea, in contrast to those of Australia, participated in early interactions with incoming Asian populations from Island Southeast Asia and continuing into Oceania.
The Indian Ocean has long been a hub of interacting human populations. Following land-and seabased routes, trade drove cultural contacts between far-distant ethnic groups in Asia, India, the Middle East and Africa, creating one of the world's first proto-globalized environments. However, the extent to which population mixing was mediated by trade is poorly understood. Reconstructing admixture times from genomic data in 3,006 individuals from 187 regional populations reveals a close associationdoi:10.1038/s41598-017-03204-y pmid:28592861 pmcid:PMC5462752 fatcat:qnna52lac5catievct7wxyx6rm
more »... etween bouts of human migration and trade volumes during the last 2,000 years across the Indian Ocean trading system. Temporal oscillations in trading activity match phases of contraction and expansion in migration, with high water marks following the expansion of the Silk Roads in the 5 th century AD, the rise of maritime routes in the 11 th century and a drastic restructuring of the trade network following the arrival of Europeans in the 16 th century. The economic fluxes of the Indian Ocean trade network therefore directly shaped exchanges of genes, in addition to goods and concepts. For more than 2,000 years, the Indian Ocean rim has been an area of intense interaction between African, Middle Eastern and Asian populations, driven by a strong tradition of wealthy maritime and land-based trading routes 1, 2 . The political unification of large territories in the third century BCE (Before Current Era) opened up new trading routes, most famously the Silk Roads and the maritime network along the coasts of the Indian Ocean 3, 4 . These in turn triggered sustained interactions between major geopolitical poles, including states in China, India, Indonesia, Arabia and East Africa 1, 5, 6 . Trade was both diverse and intense, benefiting from specialized local production, such as cotton and beads from India, gold from East Africa, spices from the Malacca city-states, incense from Yemen and silk from China 1 . With population growth and technical advances, notably in agriculture, the first century CE saw a major intensification in the movements of goods and people 3 . The development of new sailing techniques, particularly during the 11 th century CE, enabled movements over very long distance. Indonesian traders reached as far as East Africa and the Swahili city-states 7 ; Arab sailors installed trading posts on Madagascar and the west coast of India 1 ; and Chinese traded across Island Southeast Asia and East India. Far from competing, the various maritime and terrestrial routes created an intertwined and dense network that rapidly diffused goods, but also knowledge, beliefs and values, proving a unifying force across a diverse set of partners 1, 3, 6 . New urban spaces acted as hubs to the flow of trade and culture, often growing into cosmopolitan cities with large immigrant populations, such as in Baghdad and Zanzibar 8, 9 . The intensity, stability and speed of these trading connections formed a large world-system, a precursor to the heavily globalized societies of today 10 . Yet whether Indian Ocean trade directly shaped the genetics of modern populations is less well understood.
The Austronesian expansion, one of the last major human migrations, influenced regions as distant as tropical Asia, Remote Oceania and Madagascar, off the east coast of Africa. The identity of the Asian groups that settled Madagascar is particularly mysterious. While language connects Madagascar to the Ma'anyan of southern Borneo, haploid genetic data are more ambiguous. Here, we screened genomewide diversity in 211 individuals from the Ma'anyan and surrounding groups in southern Borneo.doi:10.1038/srep26066 pmid:27188237 pmcid:PMC4870696 fatcat:erykdhz7g5dhnaqebjx2lpz2qi
more »... ingly, the Ma'anyan are characterized by a distinct, high frequency genomic component that is not found in Malagasy. This novel genetic layer occurs at low levels across Island Southeast Asia and hints at a more complex model for the Austronesian expansion in this region. In contrast, Malagasy show genomic links to a range of Island Southeast Asian groups, particularly from southern Borneo, but do not have a clear genetic connection with the Ma'anyan despite the obvious linguistic association. The Austronesian expansion was a major human migration in Southeast Asia, triggered by the spread of agricultural populations approximately 5,000 years ago 1-3 . Thought to have originated in Taiwan, its influence spread through Philippines and Indonesian archipelago, ultimately impacting a wide geographical area ranging from Remote Oceania in the east, to Madagascar and the eastern coast of Africa in the west 2,4,5 . This expansion had outsized cultural and genetic impact on these territories, but the populations caught up in the dispersal were regionally different and diverse across the Indo-Pacific. This created a diverse modern range of Austronesian populations with their own cultural traits and genetic heritage, among which Madagascar is a unique case. Despite clear evidence, based on biological 6-10 and linguistic data 11,12 , of Malagasy's mixed ancestry with both African and Southeast Asian groups, identifying the parental populations of Malagasy and clarifying the process of settling Madagascar around the middle of the first millennium AD 13-15 has remained complex. Language studies have identified many linguistic characters that relate Malagasy to languages spoken in Borneo, notably in the Southeast Barito region. This includes much vocabulary and structural linguistic agreement shared between Malagasy and Southeast Barito languages, which form a subgroup of West Malayo-Polynesian languages in the Austronesian language family 11,16-21 . Among the communities speaking Southeast Barito languages, the Ma'anyan show linguistic characteristics that place them as the closest known Asian parental population to Malagasy    22, 23 . Curiously, the Ma'anyan are an indigenous ethnic group representing approximately 70,000 individuals, who live in remote inland areas of central and southeastern Kalimantan (the Indonesian part of the island of Borneo). Today, the Ma'anyan are largely agricultural, cultivating dry rice on shifting fields, but also gathering forest products 24 . They do not exhibit any particular mastery of seafaring technologies or navigational knowledge 22 , raising questions about how a closely related language travelled across the vast Indian Ocean and came to be spoken in Madagascar. However, in historical times, the south Borneo coastline was split by a gulf that may have extended 200 kilometres into the interior 25,26 , thus potentially placing Ma'anyan communities that are firmly inland today in what was then a formerly coastal environment.
Genome sequences are known for two archaic hominins-Neanderthals and Denisovans-which interbred with anatomically modern humans as they dispersed out of Africa. We identified high-confidence archaic haplotypes in 161 new genomes spanning 14 island groups in Island Southeast Asia and New Guinea and found large stretches of DNA that are inconsistent with a single introgressing Denisovan origin. Instead, modern Papuans carry hundreds of gene variants from two deeply divergent Denisovan lineagesdoi:10.1016/j.cell.2019.02.035 pmid:30981557 fatcat:lehegzieeva6lplxbstvwv6gea
more »... t separated over 350 thousand years ago. Spatial and temporal structure among these lineages suggest that introgression from one of these Denisovan groups predominantly took place east of the Wallace line and continued until near the end of the Pleistocene. A third Denisovan lineage occurs in modern East Asians. This regional mosaic suggests considerable complexity in archaic contact, with modern humans interbreeding with multiple Denisovan groups that were geographically isolated from each other over deep evolutionary time.
., , 2008 Ricaut et al., 2008) . ... Extractions were made using a modification of a previously described method (Ricaut et al., 2004) . ...doi:10.1016/j.jas.2009.12.014 fatcat:2piqbta7wrf3hhaxidusie4hxm
doi:10.1038/s41467-018-03342-5 pmid:29500350 pmcid:PMC5834599 fatcat:ijzayfbf7fapvay5cur35w2txi
doi:10.1038/ejhg.2017.88 pmid:28513608 pmcid:PMC5567155 fatcat:lzjnp3ve2zcxfl73lw3ghmtphe
Recent excavations have targeted Liang Jon (Chazine and Ferrié 2008) and Liang Abu rock shelters (Ricaut et al. 2011 (Ricaut et al. , 2012)) . ... Its di-mensions are around 25 m in maximum length and between 5 and 8 m in width (Ricaut et al. 2011) . Four test-pits were opened in 2009 and a new excavation campaign was undertaken in 2012. ...doi:10.5281/zenodo.1165929 fatcat:ajloweshzrcuhceqx3mde7ftja
Malagasy genetic diversity results from an exceptional protoglobalization process that took place over a thousand years ago across the Indian Ocean. Previous efforts to locate the Asian origin of Malagasy highlighted Borneo broadly as a potential source, but so far no firm source populations were identified. Here, we have generated genome-wide data from two Southeast Borneo populations, the Banjar and the Ngaju, together with published data from populations across the Indian Ocean region. Wedoi:10.1093/molbev/msw117 pmid:27381999 pmcid:PMC4989113 fatcat:a5ci3v2whfg4ri4smtho6o437u
more »... d strong support for an origin of the Asian ancestry of Malagasy among the Banjar. This group emerged from the long-standing presence of a Malay Empire trading post in Southeast Borneo, which favored admixture between the Malay and an autochthonous Borneo group, the Ma'anyan. Reconciling genetic, historical, and linguistic data, we show that the Banjar, in Malay-led voyages, were the most probable Asian source among the analyzed groups in the founding of the Malagasy gene pool.
Linguistic, cultural and genetic characteristics of the Malagasy suggest that both Africans and Island Southeast Asians were involved in the colonization of Madagascar. Populations from the Indonesian archipelago played an especially important role because linguistic evidence suggests that the Malagasy language branches from the Southeast Barito language family of southern Borneo, Indonesia, with the closest language spoken today by the Ma'anyan. To test for a genetic link between Malagasy anddoi:10.1186/s12864-015-1394-7 pmid:25880430 pmcid:PMC4373124 fatcat:7yxb77ct55fldpmxlspt4hizz4
more »... hese linguistically related Indonesian populations, we studied the Ma'anyan and other Indonesian ethnic groups (including the sea nomad Bajo) that, from their historical and linguistic contexts, may be modern descendants of the populations that helped enact the settlement of Madagascar. Result: A combination of phylogeographic analysis of genetic distances, haplotype comparisons and inference of parental populations by linear optimization, using both maternal and paternal DNA lineages, suggests that Malagasy derive from multiple regional sources in Indonesia, with a focus on eastern Borneo, southern Sulawesi and the Lesser Sunda islands. Conclusion: Settlement may have been mediated by ancient sea nomad movements because the linguistically closest population, Ma'anyan, has only subtle genetic connections to Malagasy, whereas genetic links with other sea nomads are more strongly supported. Our data hint at a more complex scenario for the Indonesian settlement of Madagascar than has previously been recognized.
Research of ancient pathogens in ancient human skeletons has been mainly carried out on the basis of one essential historical or archaeological observation, permitting specific pathogens to be targeted. Detection of ancient human pathogens without such evidence is more difficult, since the quantity and quality of ancient DNA, as well as the environmental bacteria potentially present in the sample, limit the analyses possible. Using human lung tissue and/or teeth samples from burials in easterndoi:10.1371/journal.pone.0021733 pmid:21765907 pmcid:PMC3135582 fatcat:r3lwdyydjbd2pomsk7yvzvgp4q
more »... iberia, dating from the end of 17 th to the 19 th century, we propose a methodology that includes the: 1) amplification of all 16S rDNA gene sequences present in each sample; 2) identification of all bacterial DNA sequences with a degree of identity $95%, according to quality criteria; 3) identification and confirmation of bacterial pathogens by the amplification of the rpoB gene; and 4) establishment of authenticity criteria for ancient DNA. This study demonstrates that from teeth samples originating from ancient human subjects, we can realise: 1) the correct identification of bacterial molecular sequence signatures by quality criteria; 2) the separation of environmental and pathogenic bacterial 16S rDNA sequences; 3) the distribution of bacterial species for each subject and for each burial; and 4) the characterisation of bacteria specific to the permafrost. Moreover, we identified three pathogens in different teeth samples by 16S rDNA sequence amplification: Bordetella sp., Streptococcus pneumoniae and Shigella dysenteriae. We tested for the presence of these pathogens by amplifying the rpoB gene. For the first time, we confirmed sequences from Bordetella pertussis in the lungs of an ancient male Siberian subject, whose grave dated from the end of the 17 th century to the early 18 th century.
doi:10.1038/ejhg.2016.60 pmid:27302840 pmcid:PMC5045871 fatcat:twp4notygrdipob6x4jvpcsx2m
Cassowaries (Casuarius) are one of the largest indigenous animal species of New Guinea. Researchers have long been trying to understand their local socio-cultural significance. Here we present new results from interviews recorded in 2018 on ethnography associated with bone daggers, a material culture ornament and tool carved from the cassowary's tibiotarsus. We present a 'storied notion'—a contemporary narrative from oral history of why cassowary is not simply a bird, and briefly describedoi:10.1017/s0959774322000026 fatcat:fyslfc4prbet7jviqcbzgem42y
more »... ary bone ornamentation in Auwim, East Sepik Province of Papua New Guinea. By exploring the material history of Casuarius through a 'storied notion' approach, we reveal that cassowary bone daggers in rock art are narrative ideas of the species from its landscape to ornamentation and through to people's cosmological beliefs surrounding Casuarius. We argue that the cassowary bone dagger stencil can be seen as part of the life history of this animal.
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