Publications by authors named "Marta Mirazón Lahr"

50 Publications

Applying dental microwear texture analysis to the living: Challenges and prospects.

Am J Phys Anthropol 2021 Mar 13;174(3):542-554. Epub 2020 Sep 13.

Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK.

Objectives: The food that people and animals consume leaves microscopic traces on teeth in predictable ways, and analyses of these markings-known as dental microwear analyses-allow us to reverse engineer the characteristics of diet. However, the microwear features of modern human diets are most often interpreted through the lens of ethnographic records. Given the subtle variation within human diets when compared to other species, we need better models of how foods and processing techniques produce marks on teeth. Here, we report on the second study to target the occlusal surface microwear of living human populations, and the first to target populations other than foragers.

Methods: We collected 150 dental impressions from five Kenyan communities: El Molo, Turkana (Kerio), Luhya (Webuye), Luhya (Port Victoria), and Luo (Port Victoria), representing a range of subsistence strategies and associated staple diets-fishing, pastoralism, and agriculture. Our results suggest that the occlusal microwear of these groups records differences in diet. However, biofilm obscured most of the molds obtained despite the steps taken to remove it, resulting in only 38 usable surfaces.

Results: Due to the biofilm problem and final sample size, the analysis did not have enough power to demonstrate the differences observed statistically. The results and problems encountered are here explained.

Conclusions: Considering that in vivo studies of dental microwear texture analysis have the potential to increase our understanding of the association between patterns of dental microwear and complex, mixed human diets, resolution of the current pitfalls of the technique is critical.
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http://dx.doi.org/10.1002/ajpa.24133DOI Listing
March 2021

Issues of theory and method in the analysis of Paleolithic mortuary behavior: A view from Shanidar Cave.

Evol Anthropol 2020 Sep 11;29(5):263-279. Epub 2020 Jul 11.

McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK.

Mortuary behavior (activities concerning dead conspecifics) is one of many traits that were previously widely considered to have been uniquely human, but on which perspectives have changed markedly in recent years. Theoretical approaches to hominin mortuary activity and its evolution have undergone major revision, and advances in diverse archeological and paleoanthropological methods have brought new ways of identifying behaviors such as intentional burial. Despite these advances, debates concerning the nature of hominin mortuary activity, particularly among the Neanderthals, rely heavily on the rereading of old excavations as new finds are relatively rare, limiting the extent to which such debates can benefit from advances in the field. The recent discovery of in situ articulated Neanderthal remains at Shanidar Cave offers a rare opportunity to take full advantage of these methodological and theoretical developments to understand Neanderthal mortuary activity, making a review of these advances relevant and timely.
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http://dx.doi.org/10.1002/evan.21854DOI Listing
September 2020

Deciphering African late middle Pleistocene hominin diversity and the origin of our species.

Nat Commun 2019 09 10;10(1):3406. Epub 2019 Sep 10.

Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Fitzwilliam Street, Cambridge, CB2 1QH, United Kingdom.

The origin of Homo sapiens remains a matter of debate. The extent and geographic patterning of morphological diversity among Late Middle Pleistocene (LMP) African hominins is largely unknown, thus precluding the definition of boundaries of variability in early H. sapiens and the interpretation of individual fossils. Here we use a phylogenetic modelling method to predict possible morphologies of a last common ancestor of all modern humans, which we compare to LMP African fossils (KNM-ES 11693, Florisbad, Irhoud 1, Omo II, and LH18). Our results support a complex process for the evolution of H. sapiens, with the recognition of different, geographically localised, populations and lineages in Africa - not all of which contributed to our species' origin. Based on the available fossils, H. sapiens appears to have originated from the coalescence of South and, possibly, East-African source populations, while North-African fossils may represent a population which introgressed into Neandertals during the LMP.
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http://dx.doi.org/10.1038/s41467-019-11213-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736881PMC
September 2019

Carbon and nitrogen isotopic signatures of hair, nail, and breath from tropical African human populations.

Rapid Commun Mass Spectrom 2019 Nov;33(22):1761-1773

Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Fitzwilliam Street, Cambridge, CB2 1QH, UK.

Rationale: Stable isotopic analyses are increasingly used to study the diets of past and present human populations. Yet, the carbon and nitrogen isotopic data of modern human diets collected so far are biased towards Europe and North America. Here, we address this gap by reporting on the dietary isotopic signatures of six tropical African communities: El Molo, Turkana (Kerio), Luhya (Webuye), Luhya (Port Victoria), and Luo (Port Victoria) from Kenya, and Baka from Cameroon; representing four subsistence strategies: fishing, pastoralism, agriculturalism, and hunter-gatherer.

Methods: We used an elemental analyser coupled in continuous-flow mode to an isotope ratio mass spectrometer to measure the carbon and nitrogen isotopic ratios of hair (n = 134) and nail (n = 80) and the carbon isotopic ratios of breath (n = 184) from these communities, as well as the carbon and nitrogen isotopic ratios of some food samples from the Kenyan communities.

Results: We expand on the known range of δ C values in human hair through the hunter-gatherer Baka, with a diet based on C plants, and through the agriculturalist Luhya (Webuye), with a diet based on C plants. In addition, we found that the consumption of fish from East African lakes is difficult to detect isotopically due to the combined effects of high nitrogen isotopic ratios of plants and the low nitrogen isotopic ratios of fish. Finally, we found that some of the communities studied are markedly changing their diets through increasing sedentism and urbanisation.

Conclusions: Our findings contribute substantially to the understanding of the environmental, demographic, and economic dynamics that affect the dietary landscape of different tropical populations of Africa. These results highlight the importance of studying a broader sample of human populations and their diet, with a focus on their precise context - from both isotopic and more general anthropological perspectives.
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http://dx.doi.org/10.1002/rcm.8524DOI Listing
November 2019

Upper Paleolithic cultural diversity in the Iranian Zagros Mountains and the expansion of modern humans into Eurasia.

J Hum Evol 2019 07 20;132:101-118. Epub 2019 May 20.

Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, The Henry Wellcome Building, 13A Fitzwilliam Street, Cambridge CB2 1QH, UK.

This paper aims to understand the cultural diversity among the first modern human populations in the Iranian Zagros and the implications of this diversity for evolutionary and ecological models of human dispersal through Eurasia. We use quantitative data and technotypological attributes combined with physiogeographic information to assess if the Zagros Upper Paleolithic (UP) developed locally from the Middle Paleolithic (MP), as well as to contextualize the variation in lithics from four UP sites of Warwasi, Yafteh, Pasangar, and Ghār-e Boof. Our results demonstrate (1) that the Zagros UP industries are intrusive to the region, and (2) that there is significant cultural diversity in the early UP across different Zagros habitat areas, and that this diversity clusters in at least three groups. We interpret this variation as parallel developments after the initial occupation of the region shaped by the relative geotopographical isolation of different areas of the Zagros, which would have favored different ecological adaptations. The greater similarity of lithic traditions and modes of production observed in the later phases of the UP across all sites indicates a marked increase in inter-group contact throughout the West-Central Zagros mountain chain. Based on the chronological and geographical patterns of Zagros UP variability, we propose a model of an initial colonization phase leading to the emergence of distinct local traditions, followed by a long phase of limited contact among these first UP groups. This has important implications for the origins of biological and cultural diversity in the early phases of modern human colonization of Eurasia. We suggest that the mountainous arc that extends from Anatolia to the Southern Zagros preserves the archaeological record of different population trajectories. Among them, by 40 ka, some would have been transient, whereas others would have left no living descendants. However, some would have led to longer term local traditions, including groups who share ancestry with modern Europeans and modern East/Southeast Asians.
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http://dx.doi.org/10.1016/j.jhevol.2019.04.002DOI Listing
July 2019

The population history of northeastern Siberia since the Pleistocene.

Nature 2019 06 5;570(7760):182-188. Epub 2019 Jun 5.

Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark.

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.
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http://dx.doi.org/10.1038/s41586-019-1279-zDOI Listing
June 2019

The not-so-dangerous lives of Neanderthals.

Nature 2018 11;563(7733):634-636

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http://dx.doi.org/10.1038/d41586-018-07343-8DOI Listing
November 2018

Early human dispersals within the Americas.

Science 2018 12 8;362(6419). Epub 2018 Nov 8.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark.

Studies of the peopling of the Americas have focused on the timing and number of initial migrations. Less attention has been paid to the subsequent spread of people within the Americas. We sequenced 15 ancient human genomes spanning from Alaska to Patagonia; six are ≥10,000 years old (up to ~18× coverage). All are most closely related to Native Americans, including those from an Ancient Beringian individual and two morphologically distinct "Paleoamericans." We found evidence of rapid dispersal and early diversification that included previously unknown groups as people moved south. This resulted in multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, as well as a later Mesoamerican-related expansion. These led to complex and dynamic population histories from North to South America.
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http://dx.doi.org/10.1126/science.aav2621DOI Listing
December 2018

Historical Tropical Forest Reliance amongst the Wanniyalaeto (Vedda) of Sri Lanka: an Isotopic Perspective.

Hum Ecol Interdiscip J 2018 24;46(3):435-444. Epub 2018 Apr 24.

Wariga Maha Gedara, Kotabakina, Dambana, Sri Lanka.

Headland and Bailey (1991) argued in that tropical forests could not support long-term human foraging in the absence of agriculture. Part of their thesis was based on the fact that supposedly isolated 'forest' foragers, such as the Wanniyalaeto (or Vedda) peoples of Sri Lanka, could be demonstrated to be enmeshed within historical trade networks and rely on crops as part of their overall subsistence. Yet, in the same volume and in the years that followed scholars have presented ethnographic and archaeological evidence, including from Sri Lanka, that counter this proposition, demonstrating the occupation and exploitation of tropical rainforest environments back to 38,000 years ago (ka) in this part of the world. However, archaeological and ethnohistorical research has yet to quantify the overall reliance of human foragers on tropical forest resources through time. Here, we report stable carbon and oxygen isotope data from historical Wanniyalaeto individuals from Sri Lanka, in full collaboration with the present-day members of this group, that suggest that while a number of individuals made use of agricultural resources in the recent past, others subsisted primarily on tropical forest resources as late as the 1800s.
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http://dx.doi.org/10.1007/s10745-018-9997-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015624PMC
April 2018

The prehistoric peopling of Southeast Asia.

Science 2018 07;361(6397):88-92

Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.

The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the "two-layer" hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.
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http://dx.doi.org/10.1126/science.aat3628DOI Listing
July 2018

Who were the Nataruk people? Mandibular morphology among late Pleistocene and early Holocene fisher-forager populations of West Turkana (Kenya).

J Hum Evol 2018 08 29;121:235-253. Epub 2018 May 29.

Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, United Kingdom; Turkana Basin Institute, Kenya. Electronic address:

Africa is the birthplace of the species Homo sapiens, and Africans today are genetically more diverse than other populations of the world. However, the processes that underpinned the evolution of African populations remain largely obscure. Only a handful of late Pleistocene African fossils (∼50-12 Ka) are known, while the more numerous sites with human fossils of early Holocene age are patchily distributed. In particular, late Pleistocene and early Holocene human diversity in Eastern Africa remains little studied, precluding any analysis of the potential factors that shaped human diversity in the region, and more broadly throughout the continent. These periods include the Last Glacial Maximum (LGM), a moment of extreme aridity in Africa that caused the fragmentation of population ranges and localised extinctions, as well as the 'African Humid Period', a moment of abrupt climate change and enhanced connectivity throughout Africa. East Africa, with its range of environments, may have acted as a refugium during the LGM, and may have played a critical biogeographic role during the heterogene`ous environmental recovery that followed. This environmental context raises a number of questions about the relationships among early Holocene African populations, and about the role played by East Africa in shaping late hunter-gatherer biological diversity. Here, we describe eight mandibles from Nataruk, an early Holocene site (∼10 Ka) in West Turkana, offering the opportunity of exploring population diversity in Africa at the height of the 'African Humid Period'. We use 3D geometric morphometric techniques to analyze the phenotypic variation of a large mandibular sample. Our results show that (i) the Nataruk mandibles are most similar to other African hunter-fisher-gatherer populations, especially to the fossils from Lothagam, another West Turkana locality, and to other early Holocene fossils from the Central Rift Valley (Kenya); and (ii) a phylogenetic connection may have existed between these Eastern African populations and some Nile Valley and Maghrebian groups, who lived at a time when a Green Sahara may have allowed substantial contact, and potential gene flow, across a vast expanse of Northern and Eastern Africa.
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http://dx.doi.org/10.1016/j.jhevol.2018.04.013DOI Listing
August 2018

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

Mol Biol Evol 2018 Mar;35(3):623-630

Estonian Biocentre, Tartu, Estonia.

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 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.
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http://dx.doi.org/10.1093/molbev/msx314DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850494PMC
March 2018

Estimating mobility using sparse data: Application to human genetic variation.

Proc Natl Acad Sci U S A 2017 11 30;114(46):12213-12218. Epub 2017 Oct 30.

Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom;

Mobility is one of the most important processes shaping spatiotemporal patterns of variation in genetic, morphological, and cultural traits. However, current approaches for inferring past migration episodes in the fields of archaeology and population genetics lack either temporal resolution or formal quantification of the underlying mobility, are poorly suited to spatially and temporally sparsely sampled data, and permit only limited systematic comparison between different time periods or geographic regions. Here we present an estimator of past mobility that addresses these issues by explicitly linking trait differentiation in space and time. We demonstrate the efficacy of this estimator using spatiotemporally explicit simulations and apply it to a large set of ancient genomic data from Western Eurasia. We identify a sequence of changes in human mobility from the Late Pleistocene to the Iron Age. We find that mobility among European Holocene farmers was significantly higher than among European hunter-gatherers both pre- and postdating the Last Glacial Maximum. We also infer that this Holocene rise in mobility occurred in at least three distinct stages: the first centering on the well-known population expansion at the beginning of the Neolithic, and the second and third centering on the beginning of the Bronze Age and the late Iron Age, respectively. These findings suggest a strong link between technological change and human mobility in Holocene Western Eurasia and demonstrate the utility of this framework for exploring changes in mobility through space and time.
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http://dx.doi.org/10.1073/pnas.1703642114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5699029PMC
November 2017

Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers.

Science 2017 11 5;358(6363):659-662. Epub 2017 Oct 5.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark.

Present-day hunter-gatherers (HGs) live in multilevel social groups essential to sustain a population structure characterized by limited levels of within-band relatedness and inbreeding. When these wider social networks evolved among HGs is unknown. To investigate whether the contemporary HG strategy was already present in the Upper Paleolithic, we used complete genome sequences from Sunghir, a site dated to ~34,000 years before the present, containing multiple anatomically modern human individuals. We show that individuals at Sunghir derive from a population of small effective size, with limited kinship and levels of inbreeding similar to HG populations. Our findings suggest that Upper Paleolithic social organization was similar to that of living HGs, with limited relatedness within residential groups embedded in a larger mating network.
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http://dx.doi.org/10.1126/science.aao1807DOI Listing
November 2017

Newly discovered Neanderthal remains from Shanidar Cave, Iraqi Kurdistan, and their attribution to Shanidar 5.

J Hum Evol 2017 10 4;111:102-118. Epub 2017 Aug 4.

McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK. Electronic address:

The Neanderthal remains from Shanidar Cave, excavated between 1951 and 1960, have played a central role in debates concerning diverse aspects of Neanderthal morphology and behavior. In 2015 and 2016, renewed excavations at the site uncovered hominin remains from the immediate area where the partial skeleton of Shanidar 5 was found in 1960. Shanidar 5 was a robust adult male estimated to have been aged over 40 years at the time of death. Comparisons of photographs from the previous and recent excavations indicate that the old and new remains were directly adjacent to one another, while the disturbed arrangement and partial crushing of the new fossils is consistent with descriptions and photographs of the older discoveries. The newly discovered bones include fragments of several vertebrae, a left hamate, part of the proximal left femur, a heavily crushed partial pelvis, and the distal half of the right tibia and fibula and associated talus and navicular. All these elements were previously missing from Shanidar 5, and morphological and metric data are consistent with the new elements belonging to this individual. A newly discovered partial left pubic symphysis indicates an age at death of 40-50 years, also consistent with the age of Shanidar 5 estimated previously. Thus, the combined evidence strongly suggests that the new finds can be attributed to Shanidar 5. Ongoing analyses of associated samples, including for sediment morphology, palynology, and dating, will therefore offer new evidence as to how this individual was deposited in the cave and permit new analyses of the skeleton itself and broader discussion of Neanderthal morphology and variation.
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http://dx.doi.org/10.1016/j.jhevol.2017.07.001DOI Listing
October 2017

New evidence suggesting a dissociated etiology for cribra orbitalia and porotic hyperostosis.

Am J Phys Anthropol 2017 09 8;164(1):76-96. Epub 2017 Jun 8.

Department of Archaeology & Anthropology, Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, United Kingdom.

Objectives: Porotic hyperostosis (PH), characterized by porotic lesions on the cranial vault, and cribra orbitalia (CO), a localized appearance of porotic lesions on the roof of the orbits, are relatively common osteological conditions. Their etiology has been the focus of several studies, and an association with anemia has long been suggested. Anemia often causes bone marrow hypertrophy or hyperplasia, leading to the expansion in trabecular or cranial diploic bone as a result of increased hematopoiesis. Hypertrophy and/or hyperplasia is often coupled with a disruption of the remodeling process of outer cortical bone, cranially and/or postcranially, leading to the externally visible porotic lesions reported in osteological remains. In this article, we investigate whether individuals with CO have increased thickness of the diploë, the common morphological direct effect of increased hematopoiesis, and thus test the relationship between the two conditions, as well as explore the type of anemia that underlie it.

Methods: An analysis of medical CT scans of a worldwide sample of 98 complete, young to middle-aged adult dry skulls from the Duckworth Collection was conducted on male and female cribrotic individuals (n = 23) and noncribrotic individuals (n = 75), all of whom lacked any evidence of porotic lesions on the vault. Measurements of total and partial cranial thickness were obtained by virtual landmark placement, using the Amira 5.4 software; all analyses were conducted in IBM SPSS 21.

Results: Cribriotic individuals have significantly thinner diploic bone and thicker outer and inner tables than noncribriotic individuals, contrary to the expected diploic expansion that would result from anemic conditions associated to bone marrow hypertrophy or hyperplasia. Additionally, individuals without CO and those with the condition have distinctive cranial thickness at particular locations across the skull and the severity to which CO is expressed also differentiates between those with mild and those with a moderate to severe form of the condition.

Conclusions: Our results suggest a complex pattern of causality in relation to the pathologies that may lead to the formation of porotic lesions on the vault and the roof of the orbits. A form of anemia may be behind the osteological changes observed in PH and CO, but it is unlikely to be the same type of anemic condition that underlies both types of osteological lesions. We suggest that CO may be associated to anemias that lead to diploic bone hypocellularity and hypoplasia, such as those caused by anemia of chronic disease and, to a lesser extent, of renal failure, aplastic anemia, protein deficiency, and anemia of endocrine disorders, and not those that lead to bone marrow hypercellularity and hyperplasia and potential PH. This leads us to the conclusion that the terms PH and CO should be used to reflect different underlying conditions.
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http://dx.doi.org/10.1002/ajpa.23258DOI Listing
September 2017

A genomic history of Aboriginal Australia.

Nature 2016 Oct 21;538(7624):207-214. Epub 2016 Sep 21.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.

The population history of Aboriginal Australians remains largely uncharacterized. Here we generate high-coverage genomes for 83 Aboriginal Australians (speakers of Pama-Nyungan languages) and 25 Papuans from the New Guinea Highlands. We find that Papuan and Aboriginal Australian ancestors diversified 25-40 thousand years ago (kya), suggesting pre-Holocene population structure in the ancient continent of Sahul (Australia, New Guinea and Tasmania). However, all of the studied Aboriginal Australians descend from a single founding population that differentiated ~10-32 kya. We infer a population expansion in northeast Australia during the Holocene epoch (past 10,000 years) associated with limited gene flow from this region to the rest of Australia, consistent with the spread of the Pama-Nyungan languages. We estimate that Aboriginal Australians and Papuans diverged from Eurasians 51-72 kya, following a single out-of-Africa dispersal, and subsequently admixed with archaic populations. Finally, we report evidence of selection in Aboriginal Australians potentially associated with living in the desert.
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http://dx.doi.org/10.1038/nature18299DOI Listing
October 2016

Genomic analyses inform on migration events during the peopling of Eurasia.

Authors:
Luca Pagani Daniel John Lawson Evelyn Jagoda Alexander Mörseburg Anders Eriksson Mario Mitt Florian Clemente Georgi Hudjashov Michael DeGiorgio Lauri Saag Jeffrey D Wall Alexia Cardona Reedik Mägi Melissa A Wilson Sayres Sarah Kaewert Charlotte Inchley Christiana L Scheib Mari Järve Monika Karmin Guy S Jacobs Tiago Antao Florin Mircea Iliescu Alena Kushniarevich Qasim Ayub Chris Tyler-Smith Yali Xue Bayazit Yunusbayev Kristiina Tambets Chandana Basu Mallick Lehti Saag Elvira Pocheshkhova George Andriadze Craig Muller Michael C Westaway David M Lambert Grigor Zoraqi Shahlo Turdikulova Dilbar Dalimova Zhaxylyk Sabitov Gazi Nurun Nahar Sultana Joseph Lachance Sarah Tishkoff Kuvat Momynaliev Jainagul Isakova Larisa D Damba Marina Gubina Pagbajabyn Nymadawa Irina Evseeva Lubov Atramentova Olga Utevska François-Xavier Ricaut Nicolas Brucato Herawati Sudoyo Thierry Letellier Murray P Cox Nikolay A Barashkov Vedrana Skaro Lejla Mulahasanovic Dragan Primorac Hovhannes Sahakyan Maru Mormina Christina A Eichstaedt Daria V Lichman Syafiq Abdullah Gyaneshwer Chaubey Joseph T S Wee Evelin Mihailov Alexandra Karunas Sergei Litvinov Rita Khusainova Natalya Ekomasova Vita Akhmetova Irina Khidiyatova Damir Marjanović Levon Yepiskoposyan Doron M Behar Elena Balanovska Andres Metspalu Miroslava Derenko Boris Malyarchuk Mikhail Voevoda Sardana A Fedorova Ludmila P Osipova Marta Mirazón Lahr Pascale Gerbault Matthew Leavesley Andrea Bamberg Migliano Michael Petraglia Oleg Balanovsky Elza K Khusnutdinova Ene Metspalu Mark G Thomas Andrea Manica Rasmus Nielsen Richard Villems Eske Willerslev Toomas Kivisild Mait Metspalu

Nature 2016 Oct 21;538(7624):238-242. Epub 2016 Sep 21.

Estonian Biocentre, Tartu, Estonia.

High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.
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http://dx.doi.org/10.1038/nature19792DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5164938PMC
October 2016

The shaping of human diversity: filters, boundaries and transitions.

Philos Trans R Soc Lond B Biol Sci 2016 07;371(1698)

Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK

The evolution of modern humans was a complex process, involving major changes in levels of diversity through time. The fossils and stone tools that record the spatial distribution of our species in the past form the backbone of our evolutionary history, and one that allows us to explore the different processes-cultural and biological-that acted to shape the evolution of different populations in the face of major climate change. Those processes created a complex palimpsest of similarities and differences, with outcomes that were at times accelerated by sharp demographic and geographical fluctuations. The result is that the population ancestral to all modern humans did not look or behave like people alive today. This has generated questions regarding the evolution of human universal characters, as well as the nature and timing of major evolutionary events in the history of Homo sapiens The paucity of African fossils remains a serious stumbling block for exploring some of these issues. However, fossil and archaeological discoveries increasingly clarify important aspects of our past, while breakthroughs from genomics and palaeogenomics have revealed aspects of the demography of Late Quaternary Eurasian hominin groups and their interactions, as well as those between foragers and farmers. This paper explores the nature and timing of key moments in the evolution of human diversity, moments in which population collapse followed by differential expansion of groups set the conditions for transitional periods. Five transitions are identified (i) at the origins of the species, 240-200 ka; (ii) at the time of the first major expansions, 130-100 ka; (iii) during a period of dispersals, 70-50 ka; (iv) across a phase of local/regional structuring of diversity, 45-25 ka; and (v) during a phase of significant extinction of hunter-gatherer diversity and expansion of particular groups, such as farmers and later societies (the Holocene Filter), 15-0 ka.This article is part of the themed issue 'Major transitions in human evolution'.
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http://dx.doi.org/10.1098/rstb.2015.0241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920297PMC
July 2016

Major transitions in human evolution.

Philos Trans R Soc Lond B Biol Sci 2016 07;371(1698)

Natural History Museum, London SW7 5BD, UK.

Evolutionary problems are often considered in terms of 'origins', and research in human evolution seen as a search for human origins. However, evolution, including human evolution, is a process of transitions from one state to another, and so questions are best put in terms of understanding the nature of those transitions. This paper discusses how the contributions to the themed issue 'Major transitions in human evolution' throw light on the pattern of change in hominin evolution. Four questions are addressed: (1) Is there a major divide between early (australopithecine) and later (Homo) evolution? (2) Does the pattern of change fit a model of short transformations, or gradual evolution? (3) Why is the role of Africa so prominent? (4) How are different aspects of adaptation-genes, phenotypes and behaviour-integrated across the transitions? The importance of developing technologies and approaches and the enduring role of fieldwork are emphasized.This article is part of the themed issue 'Major transitions in human evolution'.
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http://dx.doi.org/10.1098/rstb.2015.0229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920287PMC
July 2016

Virtual ancestor reconstruction: Revealing the ancestor of modern humans and Neandertals.

J Hum Evol 2016 Feb 29;91:57-72. Epub 2015 Dec 29.

The Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, United Kingdom; Turkana Basin Institute, Kenya.

The timing and geographic origin of the common ancestor of modern humans and Neandertals remain controversial. A poor Pleistocene hominin fossil record and the evolutionary complexities introduced by dispersals and regionalisation of lineages have fuelled taxonomic uncertainty, while new ancient genomic data have raised completely new questions. Here, we use maximum likelihood and 3D geometric morphometric methods to predict possible morphologies of the last common ancestor of modern humans and Neandertals from a simplified, fully resolved phylogeny. We describe the fully rendered 3D shapes of the predicted ancestors of humans and Neandertals, and assess their similarity to individual fossils or populations of fossils of Pleistocene age. Our results support models of an Afro-European ancestral population in the Middle Pleistocene (Homo heidelbergensis sensu lato) and further predict an African origin for this ancestral population.
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http://dx.doi.org/10.1016/j.jhevol.2015.11.002DOI Listing
February 2016

Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago.

Cell 2015 Oct 22;163(3):571-82. Epub 2015 Oct 22.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. Electronic address:

The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.
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http://dx.doi.org/10.1016/j.cell.2015.10.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4644222PMC
October 2015

Lithic landscapes: early human impact from stone tool production on the central Saharan environment.

PLoS One 2015 11;10(3):e0116482. Epub 2015 Mar 11.

Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, United Kingdom.

Humans have had a major impact on the environment. This has been particularly intense in the last millennium but has been noticeable since the development of food production and the associated higher population densities in the last 10,000 years. The use of fire and over-exploitation of large mammals has also been recognized as having an effect on the world's ecology, going back perhaps 100,000 years or more. Here we report on an earlier anthropogenic environmental change. The use of stone tools, which dates back over 2.5 million years, and the subsequent evolution of a technologically-dependent lineage required the exploitation of very large quantities of rock. However, measures of the impact of hominin stone exploitation are rare and inherently difficult. The Messak Settafet, a sandstone massif in the Central Sahara (Libya), is littered with Pleistocene stone tools on an unprecedented scale and is, in effect, a man-made landscape. Surveys showed that parts of the Messak Settafet have as much as 75 lithics per square metre and that this fractured debris is a dominant element of the environment. The type of stone tools--Acheulean and Middle Stone Age--indicates that extensive stone tool manufacture occurred over the last half million years or more. The lithic-strewn pavement created by this ancient stone tool manufacture possibly represents the earliest human environmental impact at a landscape scale and is an example of anthropogenic change. The nature of the lithics and inferred age may suggest that hominins other than modern humans were capable of unintentionally modifying their environment. The scale of debris also indicates the significance of stone as a critical resource for hominins and so provides insights into a novel evolutionary ecology.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0116482PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4356577PMC
November 2015

Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil.

Curr Biol 2014 Nov 23;24(21):R1035-7. Epub 2014 Oct 23.

Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark. Electronic address:

Understanding the peopling of the Americas remains an important and challenging question. Here, we present (14)C dates, and morphological, isotopic and genomic sequence data from two human skulls from the state of Minas Gerais, Brazil, part of one of the indigenous groups known as 'Botocudos'. We find that their genomic ancestry is Polynesian, with no detectable Native American component. Radiocarbon analysis of the skulls shows that the individuals had died prior to the beginning of the 19th century. Our findings could either represent genomic evidence of Polynesians reaching South America during their Pacific expansion, or European-mediated transport.
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http://dx.doi.org/10.1016/j.cub.2014.09.078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4370112PMC
November 2014

Paleogenomics. Genomic structure in Europeans dating back at least 36,200 years.

Science 2014 Nov 6;346(6213):1113-8. Epub 2014 Nov 6.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.

The origin of contemporary Europeans remains contentious. We obtained a genome sequence from Kostenki 14 in European Russia dating from 38,700 to 36,200 years ago, one of the oldest fossils of anatomically modern humans from Europe. We find that Kostenki 14 shares a close ancestry with the 24,000-year-old Mal'ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a metapopulation that at times stretched from Europe to central Asia.
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http://dx.doi.org/10.1126/science.aaa0114DOI Listing
November 2014

The genetic prehistory of the New World Arctic.

Science 2014 Aug;345(6200):1255832

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.

The New World Arctic, the last region of the Americas to be populated by humans, has a relatively well-researched archaeology, but an understanding of its genetic history is lacking. We present genome-wide sequence data from ancient and present-day humans from Greenland, Arctic Canada, Alaska, Aleutian Islands, and Siberia. We show that Paleo-Eskimos (~3000 BCE to 1300 CE) represent a migration pulse into the Americas independent of both Native American and Inuit expansions. Furthermore, the genetic continuity characterizing the Paleo-Eskimo period was interrupted by the arrival of a new population, representing the ancestors of present-day Inuit, with evidence of past gene flow between these lineages. Despite periodic abandonment of major Arctic regions, a single Paleo-Eskimo metapopulation likely survived in near-isolation for more than 4000 years, only to vanish around 700 years ago.
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http://dx.doi.org/10.1126/science.1255832DOI Listing
August 2014

The role of "the aquatic" in human evolution: constraining the aquatic ape hypothesis.

Evol Anthropol 2014 Mar-Apr;23(2):56-9

Few things show the distinctiveness of human evolution research better than the Aquatic Ape Hypothesis (AAH). On one hand, we have "orthodox" research into human evolution, firmly based on land; on the other, we have the aquatic ape community, convinced not only that our ancestors went through an aquatic phase, but that the professional scientific community ignores their work and keeps it out of the mainstream. How many fields of science have two entirely parallel communities that essentially are hermetically sealed from each other?
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http://dx.doi.org/10.1002/evan.21405DOI Listing
December 2014

Unravelling the distinct strains of Tharu ancestry.

Eur J Hum Genet 2014 Dec 26;22(12):1404-12. Epub 2014 Mar 26.

CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.

The northern region of the Indian subcontinent is a vast landscape interlaced by diverse ecologies, for example, the Gangetic Plain and the Himalayas. A great number of ethnic groups are found there, displaying a multitude of languages and cultures. The Tharu is one of the largest and most linguistically diverse of such groups, scattered across the Tarai region of Nepal and bordering Indian states. Their origins are uncertain. Hypotheses have been advanced postulating shared ancestry with Austroasiatic, or Tibeto-Burman-speaking populations as well as aboriginal roots in the Tarai. Several Tharu groups speak a variety of Indo-Aryan languages, but have traditionally been described by ethnographers as representing East Asian phenotype. Their ancestry and intra-population diversity has previously been tested only for haploid (mitochondrial DNA and Y-chromosome) markers in a small portion of the population. This study presents the first systematic genetic survey of the Tharu from both Nepal and two Indian states of Uttarakhand and Uttar Pradesh, using genome-wide SNPs and haploid markers. We show that the Tharu have dual genetic ancestry as up to one-half of their gene pool is of East Asian origin. Within the South Asian proportion of the Tharu genetic ancestry, we see vestiges of their common origin in the north of the South Asian Subcontinent manifested by mitochondrial DNA haplogroup M43.
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http://dx.doi.org/10.1038/ejhg.2014.36DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4231405PMC
December 2014

Evolution of the pygmy phenotype: evidence of positive selection fro genome-wide scans in African, Asian, and Melanesian pygmies.

Hum Biol 2013 Feb-Jun;85(1-3):251-84

Department of Anthropology, University College London, London, UK.

Human pygmy populations inhabit different regions of the world, from Africa to Melanesia. In Asia, short-statured populations are often referred to as "negritos." Their short stature has been interpreted as a consequence of thermoregulatory, nutritional, and/or locomotory adaptations to life in tropical forests. A more recent hypothesis proposes that their stature is the outcome of a life history trade-off in high-mortality environments, where early reproduction is favored and, consequently, early sexual maturation and early growth cessation have coevolved. Some serological evidence of deficiencies in the growth hormone/insulin-like growth factor axis have been previously associated with pygmies' short stature. Using genome-wide single-nucleotide polymorphism genotype data, we first tested whether different negrito groups living in the Philippines and Papua New Guinea are closely related and then investigated genomic signals of recent positive selection in African, Asian, and Papuan pygmy populations. We found that negritos in the Philippines and Papua New Guinea are genetically more similar to their nonpygmy neighbors than to one another and have experienced positive selection at different genes. These results indicate that geographically distant pygmy groups are likely to have evolved their short stature independently. We also found that selection on common height variants is unlikely to explain their short stature and that different genes associated with growth, thyroid function, and sexual development are under selection in different pygmy groups.
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http://dx.doi.org/10.3378/027.085.0313DOI Listing
April 2015

The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent.

PLoS Genet 2013 Nov 7;9(11):e1003912. Epub 2013 Nov 7.

Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia ; Estonian Biocentre, Tartu, Estonia.

Skin pigmentation is one of the most variable phenotypic traits in humans. A non-synonymous substitution (rs1426654) in the third exon of SLC24A5 accounts for lighter skin in Europeans but not in East Asians. A previous genome-wide association study carried out in a heterogeneous sample of UK immigrants of South Asian descent suggested that this gene also contributes significantly to skin pigmentation variation among South Asians. In the present study, we have quantitatively assessed skin pigmentation for a largely homogeneous cohort of 1228 individuals from the Southern region of the Indian subcontinent. Our data confirm significant association of rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic variation in the cohort studied. Our extensive survey of the polymorphism in 1573 individuals from 54 ethnic populations across the Indian subcontinent reveals wide presence of the derived-A allele, although the frequencies vary substantially among populations. We also show that the geospatial pattern of this allele is complex, but most importantly, reflects strong influence of language, geography and demographic history of the populations. Sequencing 11.74 kb of SLC24A5 in 95 individuals worldwide reveals that the rs1426654-A alleles in South Asian and West Eurasian populations are monophyletic and occur on the background of a common haplotype that is characterized by low genetic diversity. We date the coalescence of the light skin associated allele at 22-28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans. However, the latter also shows additional evidence of selection in populations of the Middle East, Central Asia, Pakistan and North India but not in South India.
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http://dx.doi.org/10.1371/journal.pgen.1003912DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820762PMC
November 2013