Eline D. Lorenzen
University of Copenhagen
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Featured researches published by Eline D. Lorenzen.
Nature | 2010
Morten Rasmussen; Yingrui Li; Stinus Lindgreen; Jakob Skou Pedersen; Anders Albrechtsen; Ida Moltke; Mait Metspalu; Ene Metspalu; Toomas Kivisild; Ramneek Gupta; Marcelo Bertalan; Kasper Nielsen; M. Thomas P. Gilbert; Yong Wang; Maanasa Raghavan; Paula F. Campos; Hanne Munkholm Kamp; Andrew S. Wilson; Andrew Gledhill; Silvana R. Tridico; Michael Bunce; Eline D. Lorenzen; Jonas Binladen; Xiaosen Guo; Jing Zhao; Xiuqing Zhang; Hao Zhang; Zhuo Li; Minfeng Chen; Ludovic Orlando
We report here the genome sequence of an ancient human. Obtained from ∼4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20×, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit.
Nature | 2011
Eline D. Lorenzen; David Nogués-Bravo; Ludovic Orlando; Jaco Weinstock; Jonas Binladen; Katharine A. Marske; Andrew Ugan; Michael K. Borregaard; M. Thomas P. Gilbert; Rasmus Nielsen; Simon Y. W. Ho; Ted Goebel; Kelly E. Graf; David A. Byers; Jesper Stenderup; Morten Rasmussen; Paula F. Campos; Jennifer A. Leonard; Klaus-Peter Koepfli; Duane G. Froese; Grant D. Zazula; Thomas W. Stafford; Kim Aaris-Sørensen; Persaram Batra; Alan M. Haywood; Joy S. Singarayer; Paul J. Valdes; G. G. Boeskorov; James A. Burns; Sergey P. Davydov
Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary period remain contentious. Here we use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, emphasizing the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change.
Nature | 2014
John Davison; Mari Moora; Martin Zobel; Eric Coissac; Mary E. Edwards; Eline D. Lorenzen; Mette Vestergård; Galina Gussarova; James Haile; Joseph M. Craine; Ludovic Gielly; Sanne Boessenkool; Laura Saskia Epp; Rachid Cheddadi; David W. Murray; Kari Anne Bråthen; Nigel G. Yoccoz; Heather Binney; Corinne Cruaud; Patrick Wincker; Tomasz Goslar; Inger Greve Alsos; Eva Bellemain; Anne K. Brysting; Reidar Elven; J. H. Sønstebø; Julian B. Murton; Andrei Sher; Morten Rasmussen; Regin Rønn
Although it is generally agreed that the Arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of Arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we also explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many of which became extinct around 10 kyr bp (before present). For much of the period investigated, Arctic vegetation consisted of dry steppe-tundra dominated by forbs (non-graminoid herbaceous vascular plants). During the Last Glacial Maximum (25–15 kyr bp), diversity declined markedly, although forbs remained dominant. Much changed after 10 kyr bp, with the appearance of moist tundra dominated by woody plants and graminoids. Our analyses indicate that both graminoids and forbs would have featured in megafaunal diets. As such, our findings question the predominance of a Late Quaternary graminoid-dominated Arctic mammoth steppe.
Cell | 2014
Shiping Liu; Eline D. Lorenzen; Matteo Fumagalli; Bo Li; Kelley Harris; Zijun Xiong; Long Zhou; Thorfinn Sand Korneliussen; Courtney C. Babbitt; Greg Wray; Jianwen Li; Weiming He; Zhuo Wang; Wenjing Fu; Xueyan Xiang; Claire C. Morgan; Aoife Doherty; Mary J. O’Connell; James O. McInerney; Erik W. Born; Love Dalén; Rune Dietz; Ludovic Orlando; Christian Sonne; Guojie Zhang; Rasmus Nielsen; Jun Wang
Polar bears are uniquely adapted to life in the High Arctic and have undergone drastic physiological changes in response to Arctic climates and a hyper-lipid diet of primarily marine mammal prey. We analyzed 89 complete genomes of polar bear and brown bear using population genomic modeling and show that the species diverged only 479-343 thousand years BP. We find that genes on the polar bear lineage have been under stronger positive selection than in brown bears; nine of the top 16 genes under strong positive selection are associated with cardiomyopathy and vascular disease, implying important reorganization of the cardiovascular system. One of the genes showing the strongest evidence of selection, APOB, encodes the primary lipoprotein component of low-density lipoprotein (LDL); functional mutations in APOB may explain how polar bears are able to cope with life-long elevated LDL levels that are associated with high risk of heart disease in humans.
Molecular Ecology | 2012
Eline D. Lorenzen; Rasmus Heller; Hans R. Siegismund
The savannah biome of sub‐Saharan Africa harbours the highest diversity of ungulates (hoofed mammals) on Earth. In this review, we compile population genetic data from 19 codistributed ungulate taxa of the savannah biome and find striking concordance in the phylogeographic structuring of species. Data from across taxa reveal distinct regional lineages, which reflect the survival and divergence of populations in isolated savannah refugia during the climatic oscillations of the Pleistocene. Data from taxa across trophic levels suggest distinct savannah refugia were present in West, East, Southern and South‐West Africa. Furthermore, differing Pleistocene evolutionary biogeographic scenarios are proposed for East and Southern Africa, supported by palaeoclimatic data and the fossil record. Environmental instability in East Africa facilitated several spatial and temporal refugia and is reflected in the high inter‐ and intraspecific diversity of the region. In contrast, phylogeographic data suggest a stable, long‐standing savannah refuge in the south.
Molecular Ecology | 2008
Rasmus Heller; Eline D. Lorenzen; J. B. A. Okello; Charles Masembe; Hans R. Siegismund
Genetic studies concerned with the demographic history of wildlife species can help elucidate the role of climate change and other forces such as human activity in shaping patterns of divergence and distribution. The African buffalo (Syncerus caffer) declined dramatically during the rinderpest pandemic in the late 1800s, but little is known about the earlier demographic history of the species. We analysed genetic variation at 17 microsatellite loci and a 302‐bp fragment of the mitochondrial DNA control region to infer past demographic changes in buffalo populations from East Africa. Two Bayesian coalescent‐based methods as well as traditional bottleneck tests were applied to infer detailed dynamics in buffalo demographic history. No clear genetic signature of population declines related to the rinderpest pandemic could be detected. However, Bayesian coalescent modelling detected a strong signal of African buffalo population declines in the order of 75–98%, starting in the mid‐Holocene (approximately 3–7000 years ago). The signature of decline was remarkably consistent using two different coalescent‐based methods and two types of molecular markers. Exploratory analyses involving various prior assumptions did not seriously affect the magnitude or timing of the inferred population decline. Climate data show that tropical Africa experienced a pronounced transition to a drier climate approximately 4500 years ago, concurrent with the buffalo decline. We therefore propose that the mid‐Holocene aridification of East Africa caused a major decline in the effective population size of the buffalo, a species reliant on moist savannah habitat for its existence.
Nature Ecology and Evolution | 2016
Eva Egelyng Sigsgaard; Ida Broman Nielsen; Steffen S. Bach; Eline D. Lorenzen; David P. Robinson; Steen Knudsen; Mikkel Winther Pedersen; Mohammed Al Jaidah; Ludovic Orlando; Peter Möller; Philip Francis Thomsen
Population genetics is essential for understanding and managing marine ecosystems, but sampling remains challenging. We demonstrate that high-throughput sequencing of seawater environmental DNA can provide useful estimates of genetic diversity in a whale shark (Rhincodon typus) aggregation. We recover similar mitochondrial haplotype frequencies in seawater compared to tissue samples, reliably placing the studied aggregation in a global genetic context and expanding the applications of environmental DNA to encompass population genetics of aquatic organisms.
Molecular Ecology | 2008
Eline D. Lorenzen; Peter Arctander; Hans R. Siegismund
Patterns of genetic differentiation in the plains zebra (Equus quagga) were analysed using mitochondrial DNA control region variation and seven microsatellites. The six morphologically defined subspecies of plains zebra lacked the population genetic structure indicative of distinct evolutionary units. Both marker sets showed high levels of genetic variation and very low levels of differentiation. There was no geographical structuring of mitochondrial DNA haplotypes in the phylogenetic tree, and the plains zebra showed the lowest overall differentiation recorded in any African ungulate studied so far. Arid‐adapted African ungulates have shown significant regional genetic structuring in support of the Pleistocene refuge theory. This was not the case in the zebra, and the data are discussed in relation to the impact of Pleistocene climate change on a nonbovid member of the savannah ungulate community. The only other species showing a similar absence of genetic structuring is the African buffalo (Syncerus caffer), but this taxon lacks the high levels of morphological variation present in the plains zebra.
Proceedings of the National Academy of Sciences of the United States of America | 2014
Morten E. Allentoft; Rasmus Heller; Charlotte L. Oskam; Eline D. Lorenzen; Marie L. Hale; M.T.P. Gilbert; C. Jacomb; Richard N. Holdaway; Michael Bunce
Significance In New Zealand, nine species of moa (large, wingless ratite birds) went extinct shortly after Polynesian settlement. In this study, we characterize the gene pools of four moa species during the final 4,000 y of their existence and gain new insights into moa biology and their population sizes. Our analyses show that moa populations were large and viable prior to human arrival in New Zealand, and their demise therefore represents a striking example of human overexploitation of megafauna. The extinction of New Zealands moa (Aves: Dinornithiformes) followed the arrival of humans in the late 13th century and was the final event of the prehistoric Late Quaternary megafauna extinctions. Determining the state of the moa populations in the pre-extinction period is fundamental to understanding the causes of the event. We sampled 281 moa individuals and combined radiocarbon dating with ancient DNA analyses to help resolve the extinction debate and gain insights into moa biology. The samples, which were predominantly from the last 4,000 years preceding the extinction, represent four sympatric moa species excavated from five adjacent fossil deposits. We characterized the moa assemblage using mitochondrial DNA and nuclear microsatellite markers developed specifically for moa. Although genetic diversity differed significantly among the four species, we found that the millennia preceding the extinction were characterized by a remarkable degree of genetic stability in all species, with no loss of heterozygosity and no shifts in allele frequencies over time. The extinction event itself was too rapid to be manifested in the moa gene pools. Contradicting previous claims of a decline in moa before Polynesian settlement in New Zealand, our findings indicate that the populations were large and stable before suddenly disappearing. This interpretation is supported by approximate Bayesian computation analyses. Our analyses consolidate the disappearance of moa as the most rapid, human-facilitated megafauna extinction documented to date.
Systematic Biology | 2013
Rasmus Heller; Peter Frandsen; Eline D. Lorenzen; Hans R. Siegismund
Correspondence to be sent to: Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark;E-mail: [email protected], [email protected]. Heller and P. Frandsen contributed equally to this article.Received 3 December 2012; reviews returned 7 January 2013; accepted 18 January 2013Associate Editor: Frank (Andy) Anderson