Jørgen Dissing

The genetic prehistory of the New World Arctic

Introduction Humans first peopled the North American Arctic (northern Alaska, Canada, and Greenland) around 6000 years ago, leaving behind a complex archaeological record that consisted of different cultural units and distinct ways of life, including the Early Paleo-Eskimos (Pre-Dorset/Saqqaq), the Late Paleo-Eskimos (Early Dorset, Middle Dorset, and Late Dorset), and the Thule cultures. Genetic origins of Paleo-Eskimos and Neo-Eskimos. All Paleo-Eskimos represent a single migration pulse from Siberia into the Americas, independent of the Neo-Eskimo Thule people (ancestors of modern-day Inuit) and the related extinct Sadlermiut population. The Siberian Birnirk people were likely cultural and genetic ancestors of modern-day Inuit. We also show ancient admixture between the Paleo- and Neo-Eskimo lineages, occurring at least 4000 years ago. Rationale We addressed the genetic origins and relationships of the various New World Arctic cultures to each other and to modern-day populations in the region. We obtained 26 genome-wide sequences and 169 mitochondrial DNA sequences from ancient human bone, teeth, and hair samples from Arctic Siberia, Alaska, Canada, and Greenland, and high-coverage genomes of two present-day Greenlandic Inuit, two Siberian Nivkhs, one Aleutian Islander, and two Athabascan Native Americans. Twenty-seven ancient samples were radiocarbon dated for accurate cultural assignment, of which 25 were corrected for marine reservoir effect to account for the dominant marine component in these individuals’ diets. Results Nuclear and mitochondrial DNA data unequivocally show that the Paleo-Eskimos are closer to each other than to any other present-day population. The Thule culture represents a distinct people that are genetic and cultural ancestors of modern-day Inuit. We additionally find the Siberian Birnirk culture (6th to 7th century CE) as likely cultural and genetic ancestors of the Thule. The extinct Sadlermiut people from the Hudson Bay region (15th to 19th century CE), considered to be Dorset remnants, are genetically closely related to Thule/Inuit, rather than the Paleo-Eskimos. Moreover, there is no evidence of matrilineal gene flow between Dorset or Thule groups with neighboring Norse (Vikings) populations settling in the Arctic around 1000 years ago. However, we do detect gene flow between the Paleo-Eskimo and Neo-Eskimo lineages, dating back to at least 4000 years. Conclusion Our study has a number of important implications: Paleo-Eskimos likely represent a single migration pulse into the Americas from Siberia, separate from the ones giving rise to the Inuit and other Native Americans, including Athabascan speakers. Paleo-Eskimos, despite showing cultural differences across time and space, constituted a single population displaying genetic continuity for more than 4000 years. On the contrary, the Thule people, ancestors of contemporary Inuit, represent a population replacement of the Paleo-Eskimos that occurred less than 700 years ago. The long-term genetic continuity of the Paleo-Eskimo gene pool and lack of evidence of Native American admixture suggest that the Saqqaq and Dorset people were largely living in genetic isolation after entering the New World. Thus, the Paleo-Eskimo technological innovations and changes through time, as evident from the archaeological record, seem to have occurred solely by movement of ideas within a single resident population. This suggests that cultural similarities and differences are not solid proxies for population movements and migrations into new and dramatically different environments, as is often assumed. Arctic genetics comes in from the cold Despite a well-characterized archaeological record, the genetics of the people who inhabit the Arctic have been unexplored. Raghavan et al. sequenced ancient and modern genomes of individuals from the North American Arctic (see the Perspective by Park). Analyses of these genomes indicate that the Arctic was colonized 6000 years ago by a migration separate from the one that gave rise to other Native American populations. Furthermore, the original paleo-inhabitants of the Arctic appear to have been completely replaced approximately 700 years ago. Science, this issue 10.1126/science.1255832; see also p. 1004 Early Arctic humans differed from both present-day Inuit and Native Americans. [Also see Perspective by Park] 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.

Phosphonic and arsonic acids as inhibitors of human red cell acid phosphatase and their use in affinity chromatography.

1. In order to obtain an effective ligand for affinity chromatography of the low molecular weight acid phosphatase (orthophosphoric-monoester phosphohydrolase (acid optimum), EC 3.1.3.2) from human red cells nine phosphonic and two arsonic acid substrate analogues were investigated as potential inhibitors. The two forms of acid phosphatase type B (b1 and b2) were isolated and partially purified using conventional methods and the inhibitory action of the substrate analogs investigated. 2. Four of the phosphonic acids were relatively effective competitive inhibitors. It appears that certain structural and electronic requirements have to be fulfilled by the phosphonic acids in order to exhibit significant affinity for the enzyme. A high affinity appears to require the presence of a bulky, hydrophobic moiety which has to be separated from the phosphorus atom by the distance of one atom. 3. p-Aminobenzylphosphonic acid exerted the highest affinity for acid phosphatase with a pH optimum at 6.5. Ki values of 4 . 10(-4) and 6 . 10(-4) M were found for the b1 and b2 forms, respectively. 4. Coupling of p-aminobenzylphosphonic acid to Agarose yielded an effective and specific affinity medium. By means of affinity chromatography using this medium, acid phosphatase was purified 500-fold in a single step.

Genetic Diversity among Ancient Nordic Populations

Using established criteria for work with fossil DNA we have analysed mitochondrial DNA from 92 individuals from 18 locations in Denmark ranging in time from the Mesolithic to the Medieval Age. Unequivocal assignment of mtDNA haplotypes was possible for 56 of the ancient individuals; however, the success rate varied substantially between sites; the highest rates were obtained with untouched, freshly excavated material, whereas heavy handling, archeological preservation and storage for many years influenced the ability to obtain authentic endogenic DNA. While the nucleotide diversity at two locations was similar to that among extant Danes, the diversity at four sites was considerably higher. This supports previous observations for ancient Britons. The overall occurrence of haplogroups did not deviate from extant Scandinavians, however, haplogroup I was significantly more frequent among the ancient Danes (average 13%) than among extant Danes and Scandinavians (∼2.5%) as well as among other ancient population samples reported. Haplogroup I could therefore have been an ancient Southern Scandinavian type “diluted” by later immigration events. Interestingly, the two Neolithic samples (4,200 YBP, Bell Beaker culture) that were typed were haplogroup U4 and U5a, respectively, and the single Bronze Age sample (3,300–3,500 YBP) was haplogroup U4. These two haplogroups have been associated with the Mesolithic populations of Central and Northern Europe. Therefore, at least for Southern Scandinavia, our findings do not support a possible replacement of a haplogroup U dominated hunter-gatherer population by a more haplogroup diverse Neolithic Culture.

Activity modulation of the fast and slow isozymes of human cytosolic low-molecular-weight acid phosphatase (ACP1) by purines

The activity modulation of homogeneous isozymes of the human cytosolic M(r) 18,000 acid phosphatase (ACP1) by purines has been investigated. A pronounced difference in the response of fast and slow isozymes of the same genetic type was observed, while identical properties were found for fast isozymes encoded by different alleles (ACP1 X A, B and C), as well as for the corresponding slow isozymes. The catalytic rate constant (kc) of the fast isozymes was increased 5.1-fold by hypoxanthine and decreased 40% by adenine, while the kc of the slow isozymes was unaffected by hypoxanthine but increased 4.6-fold by adenine. This finding and the genetically-determined differences in the relative quantities of the fast and slow isozymes account for the well-known phenotypic differences in activity modulation. The kinetic results strongly indicate that the effector binds to the free enzyme, as well as to the enzyme-substrate complex. Activating effectors showed a higher affinity for the free enzyme than for the enzyme-substrate complex, while the reverse was true with the inhibitor. The results exclude the possibility that effector and substrate bind to the same site of the enzyme; parasteric binding to adjacent sites is suggested.

Evidence of Authentic DNA from Danish Viking Age Skeletons Untouched by Humans for 1,000 Years

Background Given the relative abundance of modern human DNA and the inherent impossibility for incontestable proof of authenticity, results obtained on ancient human DNA have often been questioned. The widely accepted rules regarding ancient DNA work mainly affect laboratory procedures, however, pre-laboratory contamination occurring during excavation and archaeological-/anthropological handling of human remains as well as rapid degradation of authentic DNA after excavation are major obstacles. Methodology/Principal Findings We avoided some of these obstacles by analyzing DNA from ten Viking Age subjects that at the time of sampling were untouched by humans for 1,000 years. We removed teeth from the subjects prior to handling by archaeologists and anthropologists using protective equipment. An additional tooth was removed after standard archaeological and anthropological handling. All pre-PCR work was carried out in a “clean- laboratory” dedicated solely to ancient DNA work. Mitochondrial DNA was extracted and overlapping fragments spanning the HVR-1 region as well as diagnostic sites in the coding region were PCR amplified, cloned and sequenced. Consistent results were obtained with the “unhandled” teeth and there was no indication of contamination, while the latter was the case with half of the “handled” teeth. The results allowed the unequivocal assignment of a specific haplotype to each of the subjects, all haplotypes being compatible in their character states with a phylogenetic tree drawn from present day European populations. Several of the haplotypes are either infrequent or have not been observed in modern Scandinavians. The observation of haplogroup I in the present study (<2% in modern Scandinavians) supports our previous findings of a pronounced frequency of this haplogroup in Viking and Iron Age Danes. Conclusion The present work provides further evidence that retrieval of ancient human DNA is a possible task provided adequate precautions are taken and well-considered sampling is applied.

Human red cell acid phosphatase (ACP1): the primary structure of the two pairs of isozymes encoded by the ACP1*A and ACP1*C alleles

The Af, As, Cf and Cs isozymes encoded by the human red cell acid phosphatase ACP1*A and ACP1*C alleles, respectively, have been sequenced. All four isozymes consist of a single non-glycosylated peptide chain (157 residues), acetylated at the amino-terminal alanine residue. Each f isozyme differs from the corresponding s isozyme over the sequence segment 40-73, while the remaining four-fifth of the molecules are identical. These findings are consistent with results for the Bf and Bs isozymes encoded by the common ACP1*B allele and confirm that the presence of a specific f or s segment is a common property to ACP1 isozymes. This supports our hypothesis that f and s isozymes are generated by alternative splicing of exons in the primary RNA transcript. Cf and Cs are identical in sequence with Bf and Bs, respectively. Thus, the ACP1*B and ACP1*C alleles encode exactly the same pair of isozymes, the only difference at the protein level being the ratio of f and s isozyme. Af and As differ from the Bf and Bs isozymes by a single substitution at residue 105; Arg and Gln, respectively. These observations explain the electrophoretic identity of the B and C isozyme pairs and the higher P(i) of the A isozyme pair.

Human red cell acid phosphatase: purification and properties of the A, B and C isozymes

Human red cell acid phosphatase isozymes encoded by three alleles (ACP1*A, ACPI*B and ACP1*C), each of which generates two isozymes, (f) and (s), were purified to homogeneity. The molecular mass of the six isozymes (Af, As, Bf, Bs, Cf and Cs) was estimated to be 17-18 kDa, the mass of the f isozymes probably being slightly higher than that of the s isozymes. It was indicated that the isozymes react with p-nitrophenyl phosphate in the mono anionic state, and that a group with a pKa value of about 6, which may be histidine, is of importance for the catalytic function of the s isozymes. Significant differences between the f and s isozymes were observed with respect to specific activity. Km (p-nitrophenyl phosphate), Ki (p-aminobenzylphosphonic acid), amino acid composition, stability in the presence of urea, thermal stability, retention time in size-exclusion chromatography of the native isozymes and migration in sodium dodecyl sulphate polyacrylamide gel electrophoresis, In contrast, identical or similar properties were observed for the three genetically different f isozymes, and the same was the case for the three s isozymes. It is suggested that the f and s isozymes serve different functions in the cell.

Exploring the limits for the survival of DNA in blood stains

It is generally recognized that usable DNA may be retained in dry biological stains for years. We have explored the environmental limits for this property. Air-dried blood stains were incubated at different conditions of relative humidity (RH) and temperature. The quality of the extracted DNA was assessed by the ability to amplify 273 bp and 1600 bp DNA fragments by PCR, and by quantitative estimation of a 147 bp DNA fragment using real time PCR. Despite the fact that the availability of water is important for processes that degrade DNA, no significant difference was observed in the stability of DNA at 50%, 80% or 93% RH at room temperature or at 35 °C, and even the 1600 bp fragment was amplifiable after one year. Microbial growth was not observed at these conditions and the number of template molecules did not drop significantly over time. At 100% RH, however, microbial growth was observed after varying amounts of time. This may explain the decreased stability of DNA observed at these conditions. Even so, the 273 bp fragment was amplifiable for at least 3 months, and the 1600 bp fragment for at least two months. Microbial growth was not observed at higher temperatures (45-65 °C) at 100% RH, and the 1600 bp fragment was amplifiable after eight months at 45 °C, but only survived for one month at 55 °C or 65 °C. Thus DNA remains amplifiable in blood stains for many months, even at extreme RH and temperatures up to 45 °C. Even in humid climates the average RH is usually not more than 80% and RH rarely exceeds 93%; therefore we conclude that normal climatic conditions are not critical for the long time survival of DNA in untreated blood stains.

Evolutionary aspects of the gene for the classical enzyme polymorphism, ACP1

Abstract The gene for the classical polymorphic marker, ACP1, contains an unusual construction, two alternative exons, 3F and 3S, interspaced by a short 41-bp non-coding sequence, too short to function as a normal intron. During processing, two different mRNAs are produced, one containing 3F, the other 3S, resulting in the expression of two isoforms of the enzyme in human tissues. The fast and slow isoforms have different enzymatic properties and may have different physiological functions. This low molecular weight enzyme seems to function as a protein phosphotyrosine phosphatase (LMPTP). The LMPTP gene is highly conserved through evolution and has been found all the way back to yeasts, however, these express only one isoform. The ability to generate two functionally different isoforms by alternative splicing may be of evolutionary significance. We have analysed various species for LMPTP isoforms and gene structure. Two isoforms with different properties were observed in mammals and in fish, even in the evolutionary old shark. Exons similar to the human 3F and 3S were detected in cow, pig and cod, however, the intron between them is longer, 47 bp in cow and pig and 56 bp in cod.