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Chronology of natural selection in Oceanian genomes

Nicolas Brucato, Mathilde André, Georgi Hudjashov, Mayukh Mondal, Murray P. Cox, Matthew Leavesley, François-Xavier Ricaut
2022 iScience  
As human populations left Asia to first settle in Oceania around 50,000 years ago, they entered a territory ecologically separated from the Old World for millions of years. We analyzed genomic data of 239 modern Oceanian individuals to detect and date signals of selection specific to this region. Combining both relative and absolute dating approaches, we identified a strong selection pattern between 52,000 and 54,000 years ago in the genomes of descendants of the first settlers of Sahul. This
more » ... rikingly corresponds to the dates of initial settlement as inferred from archaeological evidence. Loci under selection during this period, some showing enrichment in Denisovan ancestry, overlap genes involved in the immune response and diet, especially based on plants. Pathogens and natural resources, especially from endemic plants, therefore appear to have acted as strong selective pressures on the genomes of the first settlers of Sahul.
doi:10.1016/j.isci.2022.104583 pmid:35880026 pmcid:PMC9308150 fatcat:bv4c73hbmzcotlklww4avpjokq

Late Pleistocene Complexities in the Bismarck Archipelago [chapter]

Matthew Leavesley
2008 Archaeology of Oceania: Australia and the Pacific Islands  
ACKNOWLEDGMENTS Thanks to Glenn Summerhayes, Matthew Spriggs, Peter Hiscock (Australian National University), and Christina Pavlides (LaTrobe University) for their comments on various drafts.  ...  Allen and I (Leavesley and Allen 1998 ) have identified six "pulses" of deposition representing shifts in human behavior in the New Ireland sites.  ...  Shell artifact manufacture involved a range of technologies applied to specific taxa (Leavesley and Allen 1998; Smith and Allen 1999; Wickler 1990: 140) .  ... 
doi:10.1002/9780470773475.ch9 fatcat:bzqbg7r7mzdz3lvs2ua45orlv4

Impact of Human Colonization on the Landscape: A View from the Western Pacific

Glenn R. Summerhayes, Matthew Leavesley, Andy Fairbairn
2009 Pacific Science  
It was first excavated by the late Andre Rosenfeld in 1985 (Rosenfeld 1997 as part of the Lapita Homeland Project and afterward by Matthew Leavesley in 2001 (Leavesley et al. 2002 , Leavesley and Chappell  ...  Summerhayes, 2, 4 Matthew Leavesley, 2 and Andy Fairbairn 3 Abstract: In this paper we review and assess the impact of colonizing peoples on their landscape by focusing on two very different colonizing  ... 
doi:10.2984/049.063.0412 fatcat:mlmox7rk6bdzpnw3qoiv2ywhiq

Phenotypic differences between highlanders and lowlanders in Papua New Guinea

Mathilde André, Nicolas Brucato, Sébastien Plutniak, Jason Kariwiga, John Muke, Adeline Morez, Matthew Leavesley, Mayukh Mondal, François-Xavier Ricaut, Francesc Calafell
2021 PLoS ONE  
Objectives Altitude is one of the most demanding environmental pressures for human populations. Highlanders from Asia, America and Africa have been shown to exhibit different biological adaptations, but Oceanian populations remain understudied [Woolcock et al., 1972; Cotes et al., 1974; Senn et al., 2010]. We tested the hypothesis that highlanders phenotypically differ from lowlanders in Papua New Guinea, as a result of inhabiting the highest mountains in Oceania for at least 20,000 years.
more » ... ials and methods We collected data for 13 different phenotypes related to altitude for 162 Papua New Guineans living at high altitude (Mont Wilhelm, 2,300–2,700 m above sea level (a.s.l.) and low altitude (Daru, <100m a.s.l.). Multilinear regressions were performed to detect differences between highlanders and lowlanders for phenotypic measurements related to body proportions, pulmonary function, and the circulatory system. Results Six phenotypes were significantly different between Papua New Guinean highlanders and lowlanders. Highlanders show shorter height (p-value = 0.001), smaller waist circumference (p-value = 0.002), larger Forced Vital Capacity (FVC) (p-value = 0.008), larger maximal (p-value = 3.20e -4) and minimal chest depth (p-value = 2.37e -5) and higher haemoglobin concentration (p-value = 3.36e -4). Discussion Our study reports specific phenotypes in Papua New Guinean highlanders potentially related to altitude adaptation. Similar to other human groups adapted to high altitude, the evolutionary history of Papua New Guineans appears to have also followed an adaptive biological strategy for altitude.
doi:10.1371/journal.pone.0253921 pmid:34288918 fatcat:pyikdpbu45ealhpeixdkakd6pe

Prehistoric Hunting Strategies in New Ireland, Papua New Guinea: The Evidence of the Cuscus (Phalanger orientalis) Remains from Buang Merabak Cave

Matthew G. Leavesley
2005 Asian Perspectives  
The BU:lI1g Merabak deposit was divided into four units differentiated by srra-tigraphy, chronology, and other site formation data (Leavesley 2004; Leavesley and Allen 1998) .  ...  historic hunters (Leavesley and Allen 1998: 75) and in the ethnographic present (Latinis 1996 (Latinis , 1999 Sillitoe 2003:153-193) .  ... 
doi:10.1353/asi.2005.0010 fatcat:is7zzwgycje5dmslvm77w7xyiu

Tracking ancient beach-lines inland: 2600-year-old dentate-stamped ceramics at Hopo, Vailala River region, Papua New Guinea

Robert Skelly, Bruno David, Fiona Petchey, Matthew Leavesley
2014 Antiquity  
They are only known from pre-2600 cal BP Lapita deposits at Caution Bay (David et al. 2011; McNiven et al. 2012 )-the only Robert Skelly, Bruno David, Fiona Petchey & Matthew Leavesley stratified  ...  Research Robert Skelly, Bruno David, Fiona Petchey & Matthew Leavesley Research Fingernail/other-tool-impressed decoration Two conjoining body sherds from the base of SU4 have fingernail or other  ... 
doi:10.1017/s0003598x00101127 fatcat:4q5wz3ryi5ak3pggpwbl3l52im

Rock Art and (Re)Production of Narratives: A Cassowary Bone Dagger Stencil Perspective from Auwim, East Sepik, Papua New Guinea

Roxanne Tsang, Sebastien Katuk, Sally K. May, Paul S.C. Taçon, François-Xavier Ricaut, Matthew G. Leavesley
2022 Cambridge Archaeological Journal  
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 describe
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.
doi:10.1017/s0959774322000026 fatcat:fyslfc4prbet7jviqcbzgem42y

Papuan mitochondrial genomes and the settlement of Sahul

Nicole Pedro, Nicolas Brucato, Veronica Fernandes, Mathilde André, Lauri Saag, William Pomat, Céline Besse, Anne Boland, Jean-François Deleuze, Chris Clarkson, Herawati Sudoyo, Mait Metspalu (+5 others)
2020 Journal of Human Genetics  
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 Papuan
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.
doi:10.1038/s10038-020-0781-3 pmid:32483274 fatcat:oav5cgb3nrcx5l7eog47toaepe

Multiple types of data are required to identify the mechanisms influencing the spatial expansion of melanoma cell colonies

Katrina K Treloar, Matthew J Simpson, Parvathi Haridas, Kerry J Manton, David I Leavesley, DL McElwain, Ruth E Baker
2013 BMC Systems Biology  
The expansion of cell colonies is driven by a delicate balance of several mechanisms including cell motility, cell-to-cell adhesion and cell proliferation. New approaches that can be used to independently identify and quantify the role of each mechanism will help us understand how each mechanism contributes to the expansion process. Standard mathematical modelling approaches to describe such cell colony expansion typically neglect cell-to-cell adhesion, despite the fact that cell-to-cell
more » ... n is thought to play an important role. Results: We use a combined experimental and mathematical modelling approach to determine the cell diffusivity, D, cell-to-cell adhesion strength, q, and cell proliferation rate, λ, in an expanding colony of MM127 melanoma cells. Using a circular barrier assay, we extract several types of experimental data and use a mathematical model to independently estimate D, q and λ. In our first set of experiments, we suppress cell proliferation and analyse three different types of data to estimate D and q. We find that standard types of data, such as the area enclosed by the leading edge of the expanding colony and more detailed cell density profiles throughout the expanding colony, does not provide sufficient information to uniquely identify D and q. We find that additional data relating to the degree of cell-to-cell clustering is required to provide independent estimates of q, and in turn D. In our second set of experiments, where proliferation is not suppressed, we use data describing temporal changes in cell density to determine the cell proliferation rate. In summary, we find that our experiments are best described using the range D = 161 − 243 μm 2 hour −1 , q = 0.3 − 0.5 (low to moderate strength) and λ = 0.0305 − 0.0398 hour −1 , and with these parameters we can accurately predict the temporal variations in the spatial extent and cell density profile throughout the expanding melanoma cell colony. Conclusions: Our systematic approach to identify the cell diffusivity, cell-to-cell adhesion strength and cell proliferation rate highlights the importance of integrating multiple types of data to accurately quantify the factors influencing the spatial expansion of melanoma cell colonies.
doi:10.1186/1752-0509-7-137 pmid:24330479 pmcid:PMC3878834 fatcat:u2jyxjkyl5a27lowbwgwihgdh4

Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans

Evelyn Jagoda, Daniel J Lawson, Jeffrey D Wall, David Lambert, Craig Muller, Michael Westaway, Matthew Leavesley, Terence D Capellini, Marta Mirazón Lahr, Pascale Gerbault, Mark G Thomas, Andrea Bamberg Migliano (+3 others)
2017 Molecular biology and evolution  
Recent studies have reported evidence suggesting that portions of contemporary human genomes introgressed from archaic hominin populations went to high frequencies due to positive selection. However, no study to date has specifically addressed the postintrogression population dynamics of these putative cases of adaptive introgression. Here, for the first time, we specifically define cases of immediate adaptive introgression (iAI) in which archaic haplotypes rose to high frequencies in humans as
more » ... a result of a selective sweep that occurred shortly after the introgression event. We define these cases as distinct from instances of selection on standing introgressed variation (SI), in which an introgressed haplotype initially segregated neutrally and subsequently underwent positive selection. Using a geographically diverse data set, we report novel cases of selection on introgressed variation in living humans and shortlist among these cases those whose selective sweeps are more consistent with having been the product of iAI rather than SI. Many of these novel inferred iAI haplotypes have potential biological relevance, including three that contain immune-related genes in West Siberians, South Asians, and West Eurasians. Overall, our results suggest that iAI may not represent the full picture of positive selection on archaically introgressed haplotypes in humans and that more work needs to be done to analyze the role of SI in the archaic introgression landscape of living humans.
doi:10.1093/molbev/msx314 pmid:29220488 pmcid:PMC5850494 fatcat:hi7lgnxdtvfzvg42ha3znimguy

Stochastic models support rapid peopling of Late Pleistocene Sahul

Corey J. A. Bradshaw, Kasih Norman, Sean Ulm, Alan N. Williams, Chris Clarkson, Joël Chadœuf, Sam C. Lin, Zenobia Jacobs, Richard G. Roberts, Michael I. Bird, Laura S. Weyrich, Simon G. Haberle (+7 others)
2021 Nature Communications  
AbstractThe peopling of Sahul (the combined continent of Australia and New Guinea) represents the earliest continental migration and settlement event of solely anatomically modern humans, but its patterns and ecological drivers remain largely conceptual in the current literature. We present an advanced stochastic-ecological model to test the relative support for scenarios describing where and when the first humans entered Sahul, and their most probable routes of early settlement. The model
more » ... rts a dominant entry via the northwest Sahul Shelf first, potentially followed by a second entry through New Guinea, with initial entry most consistent with 50,000 or 75,000 years ago based on comparison with bias-corrected archaeological map layers. The model's emergent properties predict that peopling of the entire continent occurred rapidly across all ecological environments within 156–208 human generations (4368–5599 years) and at a plausible rate of 0.71–0.92 km year−1. More broadly, our methods and approaches can readily inform other global migration debates, with results supporting an exit of anatomically modern humans from Africa 63,000–90,000 years ago, and the peopling of Eurasia in as little as 12,000–15,000 years via inland routes.
doi:10.1038/s41467-021-21551-3 pmid:33927195 pmcid:PMC8085232 fatcat:m5rxp5y3nvf4ve5ux62caomp3y

Archaeological Studies of the Middle and Late Holocene, Papua New Guinea. Part VIII. A preliminary study into the Lavongai rectilinear earth mounds: an XRD and phytolith analysis

Matthew G. Leavesley
2007 Technical Reports of the Australian Museum online  
LeavesLey, Matthew G., & ULrike troitzsch, 2007. Archaeological Studies of the Middle and Late Holocene, Papua New Guinea. Part VIII.  ...  , 2000 (Leavesley, , 2001 .  ... 
doi:10.3853/j.1835-4211.20.2007.1480 fatcat:wgautzizu5bfbgwih5ww6uvtry

A Preliminary Study into the Lavongai Rectilinear Earth Mounds: an XRD and Phytolith Analysis

Matthew Leavesley, Ulrike Troitzsch, Matthew Leavesley@otago, Nz
LeavesLey, Matthew G., & ULrike troitzsch, 2007. Archaeological Studies of the Middle and Late Holocene, Papua New Guinea. Part VIII.  ... 

Happiness, Wellbeing, and Mental Health in Bhutanese Higher Education: Exploring Student and Staff Experiences and Perceptions within a Framework of Gross National Happiness

Matthew J. Schuelka, University of Birmingham, Mollie Braznell, Matthew Leavesley, Sangay Dorji, Khandu Dorji, Karma Nidup, Pema Latsho, University of Birmingham, University of Birmingham, Royal University of Bhutan, Royal University of Bhutan (+2 others)
2021 Journal of International and Comparative Education  
Bhutan is a country known for happiness. In the 1970s, the Fourth Druk Gyalpo [Dragon King] of Bhutan established the development philosophy of Gross National Happiness (GNH). However, using 'happiness' as a measurement of social and economic development does not mean that all Bhutanese are 'happy' themselves. Schools -including higher education -can be stressful places in Bhutan, and there is little support or resources for the mental health and wellbeing needs of students. In this article, we
more » ... explore the experiences and perceptions of both students and staff across the Royal University of Bhutan in regard to wellbeing and mental health. In all, there were over 1,700 respondents to our survey. We explore the results of the survey through an Educational Values Evaluation and Design (EVED) framework to understand the complex factors that both enable and challenge GNH as a value in higher education. The results show that while many students view their happiness and wellbeing as positive overall, there are still a significant amount that experience depression, stress, social difficulties, and other forms of distress. In comparison to college staff perception of student's mental health and wellbeing, the students are more positive about their own wellbeing than the staff.
doi:10.14425/jice.2021.10.1.0913 fatcat:ithnby4y7ze6zldlywl3elczxi

14C Marine Reservoir Variability in Herbivores and Deposit-Feeding Gastropods from an Open Coastline, Papua New Guinea

Fiona Petchey, Sean Ulm, Bruno David, Ian J McNiven, Brit Asmussen, Helene Tomkins, Thomas Richards, Cassandra Rowe, Matthew Leavesley, Herman Mandui, John Stanisic
2012 Radiocarbon: An International Journal of Cosmogenic Isotope Research  
Herbivorous and deposit-feeding gastropods are a major component of archaeological shell middens worldwide. They provide a wealth of information about subsistence, economy, environment, and climate, but are generally considered to be less than ideal for radiocarbon dating because they can ingest sediment while they graze, inadvertently consuming terrestrial carbon in the process. However, few studies of 14C activity in herbivores or deposit-feeding gastropods have been conducted into this
more » ... e range of animals that inhabit many environmental niches. Here, we present results investigating 14C variability in shells belonging to the families Strombidae and Potamididae from the Bogi 1 archaeological site, Caution Bay, southern coastal Papua New Guinea (PNG). These shells make up 39.3% of the shell MNI in the excavation units studied and some of these species are the most common taxa of neighboring sites. It would therefore be advantageous to establish if there are any 14C offsets associated with such animals, and identify those that can give reliable calendar ages. Our methodology combines a high-resolution excavation protocol, selection of short-lived samples identified to species level, and a triisotope approach using 14C, δ13C, and δ18O to evaluate the source of variability in shells. Our results indicate that considerable variation exists between different species of Strombidae with some inhabiting muddier environments that act as sinks for limestone-derived sediments with depleted 14C content. The magnitude of variation is, however, overshadowed by that measured in the mudwhelk, Cerithidea largillierti, which has the largest spread in 14C of any shellfish studied so far at Caution Bay. This animal ingests sediment within the estuary that contains 14C derived from both enriched and depleted sources.
doi:10.1017/s0033822200047603 fatcat:5kpuv6w2mraklnq7xdzrztgel4
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