Publications by authors named "Chris Clarkson"

26 Publications

  • Page 1 of 1

Stochastic models support rapid peopling of Late Pleistocene Sahul.

Nat Commun 2021 04 29;12(1):2440. Epub 2021 Apr 29.

Global Ecology, College of Science and Engineering, Flinders University, Adelaide, SA, Australia.

The 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 supports 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. 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.
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http://dx.doi.org/10.1038/s41467-021-21551-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8085232PMC
April 2021

The genetic architecture of target-site resistance to pyrethroid insecticides in the African malaria vectors Anopheles gambiae and Anopheles coluzzii.

Mol Ecol 2021 Feb 16. Epub 2021 Feb 16.

Wellcome Sanger Institute, Cambridge, UK.

Resistance to pyrethroid insecticides is a major concern for malaria vector control. Pyrethroids target the voltage-gated sodium channel (VGSC), an essential component of the mosquito nervous system. Substitutions in the amino acid sequence can induce a resistance phenotype. We use whole-genome sequence data from phase 2 of the Anopheles gambiae 1000 Genomes Project (Ag1000G) to provide a comprehensive account of genetic variation in the Vgsc gene across 13 African countries. In addition to known resistance alleles, we describe 20 other non-synonymous nucleotide substitutions at appreciable population frequency and map these variants onto a protein model to investigate the likelihood of pyrethroid resistance phenotypes. Thirteen of these novel alleles were found to occur almost exclusively on haplotypes carrying the known L995F kdr (knock-down resistance) allele and may enhance or compensate for the L995F resistance genotype. A novel mutation I1527T, adjacent to a predicted pyrethroid-binding site, was found in tight linkage with V402L substitutions, similar to allele combinations associated with resistance in other insect species. We also analysed genetic backgrounds carrying resistance alleles, to determine which alleles have experienced recent positive selection, and describe ten distinct haplotype groups carrying known kdr alleles. Five of these groups are observed in more than one country, in one case separated by over 3000 km, providing new information about the potential for the geographical spread of resistance. Our results demonstrate that the molecular basis of target-site pyrethroid resistance in malaria vectors is more complex than previously appreciated, and provide a foundation for the development of new genetic tools for insecticide resistance management.
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http://dx.doi.org/10.1111/mec.15845DOI Listing
February 2021

Pandanus nutshell generates a palaeoprecipitation record for human occupation at Madjedbebe, northern Australia.

Nat Ecol Evol 2021 03 25;5(3):295-303. Epub 2021 Jan 25.

School of Social Science, The University of Queensland, Brisbane, Queensland, Australia.

Little is known about the Pleistocene climatic context of northern Australia at the time of early human settlement. Here we generate a palaeoprecipitation proxy using stable carbon isotope analysis of modern and archaeological pandanus nutshell from Madjedbebe, Australia's oldest known archaeological site. We document fluctuations in precipitation over the last 65,000 years and identify periods of lower precipitation during the penultimate and last glacial stages, Marine Isotope Stages 4 and 2. However, the lowest effective annual precipitation is recorded at the present time. Periods of lower precipitation, including the earliest phase of occupation, correspond with peaks in exotic stone raw materials and artefact discard at the site. This pattern is interpreted as suggesting increased group mobility and intensified use of the region during drier periods.
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http://dx.doi.org/10.1038/s41559-020-01379-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7929916PMC
March 2021

Papuan mitochondrial genomes and the settlement of Sahul.

J Hum Genet 2020 Oct 1;65(10):875-887. Epub 2020 Jun 1.

Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 route de Narbonne, Bat 4R1, 31062, Toulouse, France.

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 mitochondrial 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.
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http://dx.doi.org/10.1038/s10038-020-0781-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7449881PMC
October 2020

Human occupation of northern India spans the Toba super-eruption ~74,000 years ago.

Nat Commun 2020 02 25;11(1):961. Epub 2020 Feb 25.

School of Social Science, University of Queensland, St Lucia, QLD, 4072, Australia.

India is located at a critical geographic crossroads for understanding the dispersal of Homo sapiens out of Africa and into Asia and Oceania. Here we report evidence for long-term human occupation, spanning the last ~80 thousand years, at the site of Dhaba in the Middle Son River Valley of Central India. An unchanging stone tool industry is found at Dhaba spanning the Toba eruption of ~74 ka (i.e., the Youngest Toba Tuff, YTT) bracketed between ages of 79.6 ± 3.2 and 65.2 ± 3.1 ka, with the introduction of microlithic technology ~48 ka. The lithic industry from Dhaba strongly resembles stone tool assemblages from the African Middle Stone Age (MSA) and Arabia, and the earliest artefacts from Australia, suggesting that it is likely the product of Homo sapiens as they dispersed eastward out of Africa.
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http://dx.doi.org/10.1038/s41467-020-14668-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7042215PMC
February 2020

The first Australian plant foods at Madjedbebe, 65,000-53,000 years ago.

Nat Commun 2020 02 17;11(1):924. Epub 2020 Feb 17.

School of Social Science, University of Queensland, Brisbane, QLD, 4072, Australia.

There is little evidence for the role of plant foods in the dispersal of early modern humans into new habitats globally. Researchers have hypothesised that early movements of human populations through Island Southeast Asia and into Sahul were driven by the lure of high-calorie, low-handling-cost foods, and that the use of plant foods requiring processing was not common in Sahul until the Holocene. Here we present the analysis of charred plant food remains from Madjedbebe rockshelter in northern Australia, dated to between 65 kya and 53 kya. We demonstrate that Australia's earliest known human population exploited a range of plant foods, including those requiring processing. Our finds predate existing evidence for such subsistence practices in Sahul by at least 23ky. These results suggest that dietary breadth underpinned the success of early modern human populations in this region, with the expenditure of labour on the processing of plants guaranteeing reliable access to nutrients in new environments.
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http://dx.doi.org/10.1038/s41467-020-14723-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7026095PMC
February 2020

Whole-genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes.

Genome Res 2019 08 25;29(8):1250-1261. Epub 2019 Jul 25.

Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom.

Polymorphisms in genetic copy number can influence gene expression, coding sequence, and zygosity, making them powerful actors in the evolutionary process. Copy number variants (CNVs) are however understudied, being more difficult to detect than single-nucleotide polymorphisms. We take advantage of the intense selective pressures on the major malaria vector , caused by the widespread use of insecticides for malaria control, to investigate the role of CNVs in the evolution of insecticide resistance. Using the whole-genome sequencing data from 1142 samples in the 1000 genomes project, we identified 250 gene-containing CNVs, encompassing a total of 267 genes of which 28 were in gene families linked to metabolic insecticide resistance, representing significant enrichment of these families. The five major gene clusters for metabolic resistance all contained CNVs, with 44 different CNVs being found across these clusters and multiple CNVs frequently covering the same genes. These 44 CNVs are widespread (45% of individuals carry at least one of them) and have been spreading through positive selection, indicated by their high local frequencies and extended haplotype homozygosity. Our results demonstrate the importance of CNVs in the response to selection, highlighting the urgent need to identify the contribution of each CNV to insecticide resistance and to track their spread as the use of insecticides in malaria endemic countries intensifies and as the operational deployment of next-generation bed nets targeting metabolic resistance gathers pace. Our detailed descriptions of CNVs found across the species range provide the tools to do so.
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http://dx.doi.org/10.1101/gr.245795.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6673711PMC
August 2019

The genomics of insecticide resistance: insights from recent studies in African malaria vectors.

Curr Opin Insect Sci 2018 06 5;27:111-115. Epub 2018 Jun 5.

Big Data Institute, Oxford OX3 7FZ, United Kingdom.

Over 80% of the world's population is at risk from arthropod-vectored diseases, and arthropod crop pests are a significant threat to food security. Insecticides are our front-line response for controlling these disease vectors and pests, and consequently the increasing prevalence of insecticide resistance is of global concern. Here we provide a brief overview of how genomics can be used to implement effective insecticide resistance management (IRM), with a focus on recent advances in the study of Anopheles gambiae, the major vector of malaria in Africa. These advances unlock the potential for a predictive form of IRM, allowing tractable feedback for stakeholders, where the latest field data and well parameterised models can maximise the lifetime and effectiveness of available insecticides.
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http://dx.doi.org/10.1016/j.cois.2018.05.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6060083PMC
June 2018

Human occupation of northern Australia by 65,000 years ago.

Nature 2017 07;547(7663):306-310

Archaeology and Natural History, School of Culture, History and Language, The Australian National University, Canberra, Australian Capital Territory 2601, Australia.

The time of arrival of people in Australia is an unresolved question. It is relevant to debates about when modern humans first dispersed out of Africa and when their descendants incorporated genetic material from Neanderthals, Denisovans and possibly other hominins. Humans have also been implicated in the extinction of Australia's megafauna. Here we report the results of new excavations conducted at Madjedbebe, a rock shelter in northern Australia. Artefacts in primary depositional context are concentrated in three dense bands, with the stratigraphic integrity of the deposit demonstrated by artefact refits and by optical dating and other analyses of the sediments. Human occupation began around 65,000 years ago, with a distinctive stone tool assemblage including grinding stones, ground ochres, reflective additives and ground-edge hatchet heads. This evidence sets a new minimum age for the arrival of humans in Australia, the dispersal of modern humans out of Africa, and the subsequent interactions of modern humans with Neanderthals and Denisovans.
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http://dx.doi.org/10.1038/nature22968DOI Listing
July 2017

Identifying Major Transitions in the Evolution of Lithic Cutting Edge Production Rates.

PLoS One 2016 9;11(12):e0167244. Epub 2016 Dec 9.

School of Social Science, The University of Queensland, St Lucia, Queensland, Australia.

The notion that the evolution of core reduction strategies involved increasing efficiency in cutting edge production is prevalent in narratives of hominin technological evolution. Yet a number of studies comparing two different knapping technologies have found no significant differences in edge production. Using digital analysis methods we present an investigation of raw material efficiency in eight core technologies broadly representative of the long-term evolution of lithic technology. These are bipolar, multiplatform, discoidal, biface, Levallois, prismatic blade, punch blade and pressure blade production. Raw material efficiency is assessed by the ratio of cutting edge length to original core mass. We also examine which flake attributes contribute to maximising raw material efficiency, as well as compare the difference between expert and intermediate knappers in terms of cutting edge produced per gram of core. We identify a gradual increase in raw material efficiency over the broad sweep of lithic technological evolution. The results indicate that the most significant transition in efficiency likely took place with the introduction of small foliate biface, Levallois and prismatic blade knapping, all introduced in the Middle Stone Age / Middle Palaeolithic among early Homo sapiens and Neanderthals. This suggests that no difference in raw material efficiency existed between these species. With prismatic blade technology securely dated to the Middle Palaeolithic, by including the more recent punch and pressure blade technology our results dispel the notion that the transition to the Upper Palaeolithic was accompanied by an increase in efficiency. However, further increases in cutting edge efficiency are evident, with pressure blades possessing the highest efficiency in this study, indicating that late/epi-Palaeolithic and Neolithic blade technologies further increased efficiency.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0167244PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5147885PMC
July 2017

Early modern human lithic technology from Jerimalai, East Timor.

J Hum Evol 2016 12 10;101:45-64. Epub 2016 Nov 10.

Department of Archaeology and Natural History, The Australian National University, H.C. Coombs Building 9, Canberra, ACT 0200, Australia.

Jerimalai is a rock shelter in East Timor with cultural remains dated to 42,000 years ago, making it one of the oldest known sites of modern human activity in island Southeast Asia. It has special global significance for its record of early pelagic fishing and ancient shell fish hooks. It is also of regional significance for its early occupation and comparatively large assemblage of Pleistocene stone artefacts. Three major findings arise from our study of the stone artefacts. First, there is little change in lithic technology over the 42,000 year sequence, with the most noticeable change being the addition of new artefact types and raw materials in the mid-Holocene. Second, the assemblage is dominated by small chert cores and implements rather than pebble tools and choppers, a pattern we argue pattern, we argue, that is common in island SE Asian sites as opposed to mainland SE Asian sites. Third, the Jerimalai assemblage bears a striking resemblance to the assemblage from Liang Bua, argued by the Liang Bua excavation team to be associated with Homo floresiensis. We argue that the near proximity of these two islands along the Indonesian island chain (c.100 km apart), the long antiquity of modern human occupation in the region (as documented at Jerimalai), and the strong resemblance of distinctive flake stone technologies seen at both sites, raises the intriguing possibility that both the Liang Bua and Jerimalai assemblages were created by modern humans.
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http://dx.doi.org/10.1016/j.jhevol.2016.09.004DOI Listing
December 2016

Applicability of micro-FTIR in detecting shale heterogeneity.

J Microsc 2017 01 6;265(1):60-72. Epub 2016 Sep 6.

Department of Geoscience, University of Calgary, Calgary, Alberta, Canada.

Samples of Late Devonian/Early Mississippian New Albany Shale from the Illinois Basin, having maturities ranging from early mature to postmature, were analysed using micro-Fourier transform infrared (FTIR) spectroscopy, ImageJ processing software and scanning electron microscopic X-ray spectroscopy to explore the distribution, connectivity and chemical composition of organic matter, clay minerals, carbonate minerals and quartz, and to further test the applicability of micro-FTIR mapping to study shale heterogeneity. Each sample was analysed in planes parallel and perpendicular to the bedding to investigate anisotropy in component distribution, with a possible implication for better understanding anisotropy in porosity and permeability in organic-matter-rich shales. Our results show that for low-maturity samples, organic matter is better connected in the plane parallel to the bedding than in the plane perpendicular to the bedding. Organic matter connectivity decreases with increasing maturity as a result of kerogen transformation. Clay minerals are very well connected in both planes, whereas carbonate minerals are not abundant whilst dominantly isolated in most samples, independent of maturity. This study demonstrates that micro-FTIR mapping is a valuable tool for studying shale heterogeneity on a micrometre to millimetre scale that becomes even more powerful in combination with scanning electron microscopy techniques, which extend observations to a nanometre scale. However, to obtain meaningful and comparable results, micro-FTIR mapping requires very careful standardization, precise selection of peak heights/areas and mapping conditions (such as aperture size, scan numbers, resolution, etc.) well suited for the analysed samples.
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http://dx.doi.org/10.1111/jmi.12463DOI Listing
January 2017

The archaeology, chronology and stratigraphy of Madjedbebe (Malakunanja II): A site in northern Australia with early occupation.

J Hum Evol 2015 Jun 7;83:46-64. Epub 2015 May 7.

School of Social Science, The University of Queensland, Brisbane, Qld 4072, Australia.

Published ages of >50 ka for occupation at Madjedbebe (Malakunanja II) in Australia's north have kept the site prominent in discussions about the colonisation of Sahul. The site also contains one of the largest stone artefact assemblages in Sahul for this early period. However, the stone artefacts and other important archaeological components of the site have never been described in detail, leading to persistent doubts about its stratigraphic integrity. We report on our analysis of the stone artefacts and faunal and other materials recovered during the 1989 excavations, as well as the stratigraphy and depositional history recorded by the original excavators. We demonstrate that the technology and raw materials of the early assemblage are distinctive from those in the overlying layers. Silcrete and quartzite artefacts are common in the early assemblage, which also includes edge-ground axe fragments and ground haematite. The lower flaked stone assemblage is distinctive, comprising a mix of long convergent flakes, some radial flakes with faceted platforms, and many small thin silcrete flakes that we interpret as thinning flakes. Residue and use-wear analysis indicate occasional grinding of haematite and woodworking, as well as frequent abrading of platform edges on thinning flakes. We conclude that previous claims of extensive displacement of artefacts and post-depositional disturbance may have been overstated. The stone artefacts and stratigraphic details support previous claims for human occupation 50-60 ka and show that human occupation during this time differed from later periods. We discuss the implications of these new data for understanding the first human colonisation of Sahul.
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http://dx.doi.org/10.1016/j.jhevol.2015.03.014DOI Listing
June 2015

Does small scale structure significantly affect cosmological dynamics?

Phys Rev Lett 2015 Feb 3;114(5):051302. Epub 2015 Feb 3.

Département de Physique Théorique & Center for Astroparticle Physics, Université de Genève, Quai E. Ansermet 24, CH-1211 Genève 4, Switzerland and African Institute for Mathematical Sciences, 6 Melrose Road, Muizenberg 7945, South Africa.

The large-scale homogeneity and isotropy of the Universe is generally thought to imply a well-defined background cosmological model. It may not. Smoothing over structure adds in an extra contribution, transferring power from small scales up to large. Second-order perturbation theory implies that the effect is small, but suggests that formally the perturbation series may not converge. The amplitude of the effect is actually determined by the ratio of the Hubble scales at matter-radiation equality and today-which are entirely unrelated. This implies that a universe with significantly lower temperature today could have significant backreaction from more power on small scales, and so provides the ideal testing ground for understanding backreaction. We investigate this using two different N-body numerical simulations-a 3D Newtonian and a 1D simulation which includes all relevant relativistic effects. We show that while perturbation theory predicts an increasing backreaction as more initial small-scale power is added, in fact the virialization of structure saturates the backreaction effect at the same level independently of the equality scale. This implies that backreaction is a small effect independently of initial conditions. Nevertheless, it may still contribute at the percent level to certain cosmological observables and therefore it cannot be neglected in precision cosmology.
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http://dx.doi.org/10.1103/PhysRevLett.114.051302DOI Listing
February 2015

Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation.

Nat Commun 2014 Jun 25;5:4248. Epub 2014 Jun 25.

1] Department of Vector Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK [2] Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1RQ, UK.

Adaptive introgression can provide novel genetic variation to fuel rapid evolutionary responses, though it may be counterbalanced by potential for detrimental disruption of the recipient genomic background. We examine the extent and impact of recent introgression of a strongly selected insecticide-resistance mutation (Vgsc-1014F) located within one of two exceptionally large genomic islands of divergence separating the Anopheles gambiae species pair. Here we show that transfer of the Vgsc mutation results in homogenization of the entire genomic island region (~1.5% of the genome) between species. Despite this massive disruption, introgression is clearly adaptive with a dramatic rise in frequency of Vgsc-1014F and no discernable impact on subsequent reproductive isolation between species. Our results show (1) how resilience of genomes to massive introgression can permit rapid adaptive response to anthropogenic selection and (2) that even extreme prominence of genomic islands of divergence can be an unreliable indicator of importance in speciation.
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http://dx.doi.org/10.1038/ncomms5248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086683PMC
June 2014

Genomics and the origin of species.

Nat Rev Genet 2014 Mar;15(3):176-92

Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.

Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics.
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http://dx.doi.org/10.1038/nrg3644DOI Listing
March 2014

Antilensing: the bright side of voids.

Phys Rev Lett 2013 Jan 10;110(2):021302. Epub 2013 Jan 10.

Sydney Institute for Astronomy, The University of Sydney, Sydney, New South Wales 2006, Australia.

More than half of the volume of our Universe is occupied by cosmic voids. The lensing magnification effect from those underdense regions is generally thought to give a small dimming contribution: objects on the far side of a void are supposed to be observed as slightly smaller than if the void were not there, which together with conservation of surface brightness implies net reduction in photons received. This is predicted by the usual weak lensing integral of the density contrast along the line of sight. We show that this standard effect is swamped at low redshifts by a relativistic Doppler term that is typically neglected. Contrary to the usual expectation, objects on the far side of a void are brighter than they would be otherwise. Thus the local dynamics of matter in and near the void is crucial and is only captured by the full relativistic lensing convergence. There are also significant nonlinear corrections to the relativistic linear theory, which we show actually underpredicts the effect. We use exact solutions to estimate that these can be more than 20% for deep voids. This remains an important source of systematic errors for weak lensing density reconstruction in galaxy surveys and for supernovae observations, and may be the cause of the reported extra scatter of field supernovae located on the edge of voids compared to those in clusters.
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http://dx.doi.org/10.1103/PhysRevLett.110.021302DOI Listing
January 2013

Hominin dispersal into the Nefud Desert and Middle palaeolithic settlement along the Jubbah Palaeolake, Northern Arabia.

PLoS One 2012 19;7(11):e49840. Epub 2012 Nov 19.

School of Archaeology, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom.

The Arabian Peninsula is a key region for understanding hominin dispersals and the effect of climate change on prehistoric demography, although little information on these topics is presently available owing to the poor preservation of archaeological sites in this desert environment. Here, we describe the discovery of three stratified and buried archaeological sites in the Nefud Desert, which includes the oldest dated occupation for the region. The stone tool assemblages are identified as a Middle Palaeolithic industry that includes Levallois manufacturing methods and the production of tools on flakes. Hominin occupations correspond with humid periods, particularly Marine Isotope Stages 7 and 5 of the Late Pleistocene. The Middle Palaeolithic occupations were situated along the Jubbah palaeolake-shores, in a grassland setting with some trees. Populations procured different raw materials across the lake region to manufacture stone tools, using the implements to process plants and animals. To reach the Jubbah palaeolake, Middle Palaeolithic populations travelled into the ameliorated Nefud Desert interior, possibly gaining access from multiple directions, either using routes from the north and west (the Levant and the Sinai), the north (the Mesopotamian plains and the Euphrates basin), or the east (the Persian Gulf). The Jubbah stone tool assemblages have their own suite of technological characters, but have types reminiscent of both African Middle Stone Age and Levantine Middle Palaeolithic industries. Comparative inter-regional analysis of core technology indicates morphological similarities with the Levantine Tabun C assemblage, associated with human fossils controversially identified as either Neanderthals or Homo sapiens.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0049840PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3501467PMC
May 2013

Isotropic blackbody cosmic microwave background radiation as evidence for a homogeneous universe.

Phys Rev Lett 2012 Aug 1;109(5):051303. Epub 2012 Aug 1.

School of Physics and Astronomy, Queen Mary University of London, United Kingdom.

The question of whether the Universe is spatially homogeneous and isotropic on the largest scales is of fundamental importance to cosmology but has not yet been answered decisively. Surprisingly, neither an isotropic primary cosmic microwave background (CMB) nor combined observations of luminosity distances and galaxy number counts are sufficient to establish such a result. The inclusion of the Sunyaev-Zel'dovich effect in CMB observations, however, dramatically improves this situation. We show that even a solitary observer who sees an isotropic blackbody CMB can conclude that the Universe is homogeneous and isotropic in their causal past when the Sunyaev-Zel'dovich effect is present. Critically, however, the CMB must either be viewed for an extended period of time, or CMB photons that have scattered more than once must be detected. This result provides a theoretical underpinning for testing the cosmological principle with observations of the CMB alone.
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http://dx.doi.org/10.1103/PhysRevLett.109.051303DOI Listing
August 2012

Pelagic fishing at 42,000 years before the present and the maritime skills of modern humans.

Science 2011 Nov;334(6059):1117-21

Department of Archaeology and Natural History, College of Asia and the Pacific, Australian National University, Canberra, Australian Capital Territory 0200, Australia.

By 50,000 years ago, it is clear that modern humans were capable of long-distance sea travel as they colonized Australia. However, evidence for advanced maritime skills, and for fishing in particular, is rare before the terminal Pleistocene/early Holocene. Here we report remains of a variety of pelagic and other fish species dating to 42,000 years before the present from Jerimalai shelter in East Timor, as well as the earliest definite evidence for fishhook manufacture in the world. Capturing pelagic fish such as tuna requires high levels of planning and complex maritime technology. The evidence implies that the inhabitants were fishing in the deep sea.
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http://dx.doi.org/10.1126/science.1207703DOI Listing
November 2011

Direct reconstruction of dark energy.

Phys Rev Lett 2010 May 27;104(21):211301. Epub 2010 May 27.

Centre for Astrophysics, Cosmology & Gravitation, University of Cape Town, South Africa.

An important issue in cosmology is reconstructing the effective dark energy equation of state directly from observations. With so few physically motivated models, future dark energy studies cannot only be based on constraining a dark energy parameter space. We present a new nonparametric method which can accurately reconstruct a wide variety of dark energy behavior with no prior assumptions about it. It is simple, quick and relatively accurate, and involves no expensive explorations of parameter space. The technique uses principal component analysis and a combination of information criteria to identify real features in the data, and tailors the fitting functions to pick up trends and smooth over noise. We find that we can constrain a large variety of w(z) models to within 10%-20% at redshifts z≲1 using just SNAP-quality data.
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http://dx.doi.org/10.1103/PhysRevLett.104.211301DOI Listing
May 2010

Out of Africa: new hypotheses and evidence for the dispersal of Homo sapiens along the Indian Ocean rim.

Ann Hum Biol 2010 Jun;37(3):288-311

School of Archaeology, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, UK.

The dispersal of Homo sapiens out of Africa is a significant topic in human evolutionary studies. Most investigators agree that our species arose in Africa and subsequently spread out to occupy much of Eurasia. Researchers have argued that populations expanded along the Indian Ocean rim at ca 60,000 years ago during a single rapid dispersal event, probably employing a coastal route towards Australasia. Archaeologists have been relatively silent about the movement and expansion of human populations in terrestrial environments along the Indian Ocean rim, although it is clear that Homo sapiens reached Australia by ca 45,000 years ago. Here, we synthesize and document current genetic and archaeological evidence from two major landmasses, the Arabian peninsula and the Indian subcontinent, regions that have been underplayed in the story of out of Africa dispersals. We suggest that modern humans were present in Arabia and South Asia earlier than currently believed, and probably coincident with the presence of Homo sapiens in the Levant between ca 130 and 70,000 years ago. We show that climatic and environmental fluctuations during the Late Pleistocene would have had significant demographic effects on Arabian and South Asian populations, though indigenous populations would have responded in different ways. Based on a review of the current genetic, archaeological and environmental data, we indicate that demographic patterns in Arabia and South Asia are more interesting and complex than surmised to date.
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http://dx.doi.org/10.3109/03014461003639249DOI Listing
June 2010

Consistency tests for the cosmological constant.

Phys Rev Lett 2008 Oct 31;101(18):181301. Epub 2008 Oct 31.

Oxford University, Astrophysics, Denys Wilkinson Building, Keble Road, OX1 3RH, United Kingdom.

We propose consistency tests for the cosmological constant which provide a direct observational signal if Lambda is wrong, regardless of the densities of matter and curvature. As an example of its utility, our flat case test can warn of a small transition of the equation of state w(z) from w(z)=-1 of 20% from SNAP (Supernova Acceleration Probe) quality data at 4-sigma, even when direct reconstruction techniques see virtually no evidence for deviation from Lambda. It is shown to successfully rule out a wide range of non-Lambda dark energy models with no reliance on knowledge of Omega_{m} using SNAP quality data and a large range for using 10;{5} supernovae as forecasted for the Large Synoptic Survey Telescope.
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http://dx.doi.org/10.1103/PhysRevLett.101.181301DOI Listing
October 2008

A general test of the Copernican principle.

Phys Rev Lett 2008 Jul 2;101(1):011301. Epub 2008 Jul 2.

Cosmology and Gravity Group, Department of Mathematics and Applied Mathematics, University of Cape Town, Rondebosch 7701, South Africa.

To date, there has been no general way of determining if the Copernican principle--that we live at a typical position in the Universe--is in fact a valid assumption, significantly weakening the foundations of cosmology as a scientific endeavor. Here we present an observational test for the Copernican assumption which can be automatically implemented while we search for dark energy in the coming decade. Our test is entirely independent of any model for dark energy or theory of gravity and thereby represents a model-independent test of the Copernican principle.
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http://dx.doi.org/10.1103/PhysRevLett.101.011301DOI Listing
July 2008

Time drift of cosmological redshifts as a test of the Copernican principle.

Phys Rev Lett 2008 May 16;100(19):191303. Epub 2008 May 16.

Institut d'Astrophysique de Paris, Université Pierre and Marie Curie-Paris VI, CNRS-UMR 7095, Paris, France.

We present the time drift of the cosmological redshift in a general spherically symmetric spacetime. We demonstrate that its observation would allow us to test the Copernican principle and so determine if our Universe is radially inhomogeneous, an important issue in our understanding of dark energy. In particular, when combined with distance data, this extra observable allows one to fully reconstruct the geometry of a spacetime describing a spherically symmetric underdense region around us, purely from background observations.
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http://dx.doi.org/10.1103/PhysRevLett.100.191303DOI Listing
May 2008

Detecting extra dimensions with gravity-wave spectroscopy: the black-string brane world.

Phys Rev Lett 2005 Apr 1;94(12):121302. Epub 2005 Apr 1.

Institute of Cosmology & Gravitation, University of Portsmouth, Portsmouth PO1 2EG, United Kingdom.

Using the black string between two branes as a model of a brane-world black hole, we compute the gravity-wave perturbations and identify the features arising from the additional polarizations of the graviton. The standard four-dimensional gravitational wave signal acquires late-time oscillations due to massive modes of the graviton. The Fourier transform of these oscillations shows a series of spikes associated with the masses of the Kaluza-Klein modes, providing in principle a spectroscopic signature of extra dimensions.
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http://dx.doi.org/10.1103/PhysRevLett.94.121302DOI Listing
April 2005