Результаты исследования древней ДНК (дДНК)

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Было проведено полномасштабное исследование древних ДНК из "Лихтенштейнской пещеры". Найденные в пещере артифакты принадлежат периоду 700-1000 лет до н. э.

Были изучены 21 женский и 19 мужских скелетов и проведен полный спектр генетических исследований:

1) Аутосомный профиль по системе CODIS и ССR5

17 образцов были тестированы на CCR5. 2 муж. и 2 жен. образца оказались CCR5 del32 и все 4 образца гетерозиготны.

2) мтДНК (HVR1-HVR2)

47% - H (17 обр.)
25% - U (9)
14% - J (5)
14% - T (5)

3) уДНК (12 локусов Y-хромосомы) - 15 гаплотипов (!)

80% - I2b
14% - R1a
7% - R1b1b


* Я перевел всё в фортам ftdna плюс гаплогруппы по предиктору с 95-100% вероятностью

Помимо всего были составлены генеалогические схемы родства (см. в источнике)

Felix Schilz - Molekulargenetische Verwandtschaftsanalysen am pr?historischen Skelettkollektiv der Lichtensteinh?hle // G?ttingen 2006 (9mb)

http://en.wikipedia.org/wiki/Urnfield_Culture

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К великому сожалению так долго ожидавшаяся работа по дДНК из микенских захоронений выходит без Y и аутосомных днк - тут их постигла неудача  *10

Abigail S et al. - Kinship between burials from Grave Circle B at Mycenae revealed by ancient DNA typing // Journal of Archaeological Science

Исследовали только мтДНК.

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Одна из первых масштабных работ по снипам дДНК

эх... многие бы культуры так

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Кроманьонцы, (24000 до н э)
mtDNA - H

Кроманьонцы, (22000 до н э)
mtDNA - HV (pre-HV?), N*

Аляска (8300 до н э)
yDNA - Q1a3a
mtDNA - D

Чеддерский Чел, Англия (6000 до н э)
mtDNA - U5a

Первые фермеры, ц. Европа, 5500 до н э
mtDNA - N1a(6), T(5), H, K(4), J(1), U3(1)

Афанасьевцы (3500–2500 до н э)
mtDNA - N1a, T

Otzi, итальянские Альпы (3350-3300 до н э)
mtDNA - K1

Германия, Eulau (2600 до н э)
yDNA - R1a(3)
mtDNA - K1b(3), K1a2, H, I, U5b, X2(2)

Андроновцы (2300–1000 до н э)
yDNA - R1a1
mtDNA - T1, U4, U2e, H?, K, U5a1

Скифы, Сибирь (1500 до н э)
mtDNA - N1a

Германия (1000 до н  э)
yDNA - R1b1b2, I1b2, R1a1
mtDNA - H*(17), U*(9), J*(5), T*(5)

Тагарцы (800–200 до н э)
yDNA - R1a1

Этруски (5-2 вв до н э)
mtDNA - H, J1, J2, U (?)

Пазырыкская культура (4-2 вв. до н э)
mtDNA - HV(принцесса), C(воин), U5(воин), C, D, C, H(4 образца)

Монгол, (3 в до н э)
yDNA - N1c (TAT)

Таштыкцы (200 до н э–200)
yDNA - R1a1

Монголия, могильник (2000 лет назад)
mtDNA - A, B4b, C(6), D4(17), U2, D5(2), G2a, F1b(4), J1(2), M(2), U5a1a(2)

Баски (6-7 в н э)
mtDNA - H(3), V, T2(2), T, U5(3), U2(2), K, J(3), M1

Бавария, Ergolding (период Меровингов) 7 век
уDNA - R1b1b2(4), G2a(2)

Дания, 1000-1250 гг
mtDNA - H(3), I(2), U7(1), J(1), T2(1), T(1)

Половцы, район Карпат, 13 в.
mtDNA - H(4), U(2), V(2), JT(1), U3, D

Король датских викингов Свен Естридсен (ум.1074 г)
mtDNA - H5a

Лука Евангилист (?)
mtDNA - H

Англо-саксон (11 век)
mtDNA - X

Мария Антуанетта
mtDNA - H

Франческа Петрарка (14 века)
mtDNA - J2

Вологодская обл., могильники 12-13 вв
mtDNA - H, I

Николай Коперник
mtDNA - H
yDNA - R1b1b2

Николай Романов
mtDNA - T
yDNA - R1b1b2

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Ancient DNA, Strontium isotopes, and osteological analyses shed light on social and kinship organization of the Later Stone Age

Wolfgang Haak et al 2008

Abstract

In 2005 four outstanding multiple burials were discovered near Eulau, Germany. The 4,600-year-old graves contained groups of adults and children buried facing each other. Skeletal and artifactual evidence and the simultaneous interment of the individuals suggest the supposed families fell victim to a violent event. In a multidisciplinary approach, archaeological, anthropological, geochemical (radiogenic isotopes), and molecular genetic (ancient DNA) methods were applied to these unique burials. Using autosomal, mitochondrial, and Y-chromosomal markers, we identified genetic kinship among the individuals. A direct child-parent relationship was detected in one burial, providing the oldest molecular genetic evidence of a nuclear family. Strontium isotope analyses point to different origins for males and children versus females. By this approach, we gain insight into a Late Stone Age society, which appears to have been exogamous and patrilocal, and in which genetic kinship seems to be a focal point of social organization.

http://www.pnas.org/content/early/2008/11/...807592105.short
http://www.pnas.org/content/suppl/2008/11/...807592105SI.pdf

http://maps.google.com/maps?f=q&hl=en&....824219&z=5

Наиболее полный гаплотип в формате Y12:
R1a 14-25-16-11-11-XX-XX-XX-10-13-XX-30

The Y haplotype was predicted using the Web-based program Haplotype
Predictor (9). The three individuals of grave 99 belong to
haplotype R1a, with a probability of 100% based on the Y-STR
profile of individual 3 (10). To confirm haplogroup status, we
further amplified an 85-bp fragment covering the Y-SNP marker
SRY10831.2 characteristic for R1a (11).

mtDNA
CWC individuals from Eulau
99–1 16093C, 16224C, 16311C, 16319A n.a. K1b
99–2 16093C, 16224C, 16311C, 16319A n.a. K1b
99–3 16189C, 16192T, 16270T n.a. U5b
99–4 16093C, 16224C, 16311C, 16319A n.a. K1b
90–5 16129A, 16223T, 16391A n.a. I
98–7 16093C, 16221T n.a. H
98–9 16189C, 16223T, 16278T 73G, 153G, 195C, 225A, 226C, 263G X2
98–10 16189C, 16223T, 16278T 73G, 153G, 195C, 225A, 226C, 263G X2
93–13 16145A, 16224C, 16311C n.a. K1a2

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Ancient DNA and Family Relationships in a Pompeian House // Annals of Human Genetics, Published Online: 28 May 2009

Giovanni  Di Bernardo et al

ABSTRACT

Archaeological, anthropological and pathological data suggest that thirteen skeletons found in a house at the Pompeii archaeological site, dated to 79 A.D., belong to one family. To verify this and to identify the relationships between these individuals, we analyzed DNA extracted from bone specimens. Specifically, hypervariable segment 1 (HVS1) of the human mitochondrial DNA (mtDNA) control region was amplified in two overlapping polymerase chain reactions and the sequences were compared to the revised Cambridge Reference Sequence. As independent controls, other polymorphic sites in HVS1, HVS2 and in the coding region were analyzed. We also amplified some short tandem repeats of the thirteen specimens. This study revealed that six of the thirteen individuals are indeed closely related.

http://www3.interscience.wiley.com/journal/122410239/abstract

6/13 T2b

Skeleton    HVS1     
   MIT A/B b   MIT C/Dc
1A   rCRS   16399
1B   16292,16298   16292,16298
2A   16292,16298   16292,16298
2B   16292,16298   16292,16298
2C   16292,16298   16292,16298
3A   16292,16298   16292,16298
3B   16292,16298   16292,16298
3C   d   d
3D   16294,16304   16294,16304
3E   16291   16390
4A   rCRS   rCRS
5,6A   rCRS   16391
5,6B   rCRS    rCRS

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Kinship and Y-Chromosome Analysis of 7th Century Human Remains: Novel DNA Extraction and Typing Procedure for Ancient Material // Croat Med J. 2009 Jun;50(3):286-95

Vanek et al

http://www.cmj.hr/2009/50/3/19480023.htm

4/6 R1b1b2
2/6 G2a

Сделаны гаплотипы по 26 локусам (не полные).

Sample YSEARCH identifier

244A/244B 6QUDR
244C H78RA
244D ZYRUU
244E* H6KZ2, QCX3T
244F 2SRMA

The grave 244 makes this place one of the richest Bavarian burial sites from the late-Merowig period. The grave 244 dates to the period around 670 AD.

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Genetic identification of putative remains of the famous astronomer Nicolaus Copernicus

Wies?aw Bogdanowicz et al.

Abstract

We report the results of mitochondrial and nuclear DNA analyses of skeletal remains exhumed in 2005 at Frombork Cathedral in Poland, that are thought to be those of Nicolaus Copernicus (1473–1543). The analyzed bone remains were found close to the altar Nicolaus Copernicus was responsible for during his tenure as priest. The mitochondrial DNA (mtDNA) profiles from 3 upper molars and the femurs were identical, suggesting that the remains originate from the same individual. Identical mtDNA profiles were also determined in 2 hairs discovered in a calendar now exhibited at Museum Gustavianum in Uppsala, Sweden. This calendar was the property of Nicolaus Copernicus for much of his life. These findings, together with anthropological data, support the identification of the human remains found in Frombork Cathedral as those of Nicolaus Copernicus. Up-to-now the particular mtDNA haplotype has been observed only 3 times in Germany and once in Denmark. Moreover, Y-chromosomal and autosomal short tandem repeat markers were analyzed in one of the tooth samples, that was much better preserved than other parts of the skeleton. Molecular sex determination revealed that the skeleton is from a male individual, and this result is consistent with morphological investigations. The minimal Y-chromosomal haplotype determined in the putative remains of Nicolaus Copernicus has been observed previously in many countries, including Austria, Germany, Poland, and the Czech Republic. Finally, an analysis of the SNP located in the HERC2 gene revealed the C/C genotype that is predominant in blue-eyed humans, suggesting that Copernicus may have had a light iris color.

http://www.pnas.org/content/early/2009/07/06/0901848106.abstract

H -

709G, 1719G, 1811A, 3010G, 6365T, 6776T, 7028C, 8251G, 8697G, 9055G,11251A, 12372G, 13708G, 14766C, 14798T, and 15904C

R1b1b -
 
DYS456–16;
DYS389I– 13;
DYS390– 23;
DYS389II– 29;
DYS458– 19;
DYS19– 14;
DYS385– 11, 13;
DYS393– 13;
DYS391– 11;
DYS439– 12;
DYS635– 23;
DYS392–13;
Y GATA H4– 12;
DYS437– 15;
DYS438– 12;
DYS448– 19

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Demographic history of Canary Islands male gene-pool: replacement of native lineages by Europea // BMC Evolutionary Biology 2009, 9:181 doi:10.1186/1471-2148-9-181

Rosa Fregel et al.

The origin and prevalence of the prehispanic settlers of the Canary Islands has attracted great multidisciplinary interest. However, direct ancient DNA genetic studies on indigenous and historical 17th-18th century remains, using mitochondrial DNA as a female marker, have only recently been possible. In the present work, the analysis of Y-chromosome polymorphisms in the same samples, has shed light on the way the European colonization affected male and female Canary Island indigenous genetic pools, from the conquest to present-day times.

http://www.biomedcentral.com/content/pdf/1471-2148-9-181.pdf

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Genetic analysis of early holocene skeletal remains from Alaska and its implications for the settlement of the Americas // Am J Phys Anthropol. 2007 Apr;132(4):605-21

Kemp et al.

Mitochondrial and Y-chromosome DNA were analyzed from 10,300-year-old human remains excavated from On Your Knees Cave on Prince of Wales Island, Alaska (Site 49-PET-408). This individual's mitochondrial DNA (mtDNA) represents the founder haplotype of an additional subhaplogroup of haplogroup D that was brought to the Americas, demonstrating that widely held assumptions about the genetic composition of the earliest Americans are incorrect. The amount of diversity that has accumulated in the subhaplogroup over the past 10,300 years suggests that previous calibrations of the mtDNA clock may have underestimated the rate of molecular evolution. If substantiated, the dates of events based on these previous estimates are too old, which may explain the discordance between inferences based on genetic and archaeological evidence regarding the timing of the settlement of the Americas. In addition, this individual's Y-chromosome belongs to haplogroup Q-M3*, placing a minimum date of 10,300 years ago for the emergence of this haplogroup.

http://www.ncbi.nlm.nih.gov/pubmed/17243155?dopt=AbstractPlus
http://www.sjdimond.us/document/2007_AlaskanRemains.pdf

Y-ДНК: Q1a3a*  (M3)
мтДНК: D4h3 (16092, 16223, 16241, 16301, 16342, 16362, 00073, 00152, 00263, 00309.1, 00315, 00489)

[Аббат Бузони]

Genetic Discontinuity Between Local Hunter-Gatherers and Central Europe's First Farmers
B. Bramanti et al

Science
Published Online September 3, 2009

http://www.sciencemag.org/cgi/content/abstract/1176869v1

Following the domestication of animals and crops in the Near East some 11,000 years ago, farming reached much of Central Europe by 7,500 years before present. The extent to which these early European farmers were immigrants, or descendants of resident hunter-gatherers who had adopted farming, has been widely debated. We compare new mitochondrial DNA (mtDNA) sequences from late European hunter-gatherer skeletons with those from early farmers, and from modern Europeans. We find large genetic differences between all three groups that cannot be explained by population continuity alone. Most (82%) of the ancient hunter-gatherers share mtDNA types that are relatively rare in Central Europeans today. Together, these analyses provide persuasive evidence that the first farmers were not the descendants of local hunter-gatherers but immigrated into Central Europe at the onset of the Neolithic.

Сапплемент доступен бесплатно здесь

http://www.sciencemag.org/cgi/data/1176869/DC1/1

Почти все донеолитические типы - U5 и U4.

Germany
1. Ostorf: 3200 BC - mtDNA K; 3200 BC - U5; 3100 BC - U5; 3000 BC - T2e; 3000 BC - J; 3000 BC - T2e; 2950 BC - U5a.
2. Bad DD?rrenberg: ca. 6850 BC - U4;
3. Falkensteiner HH?hle: 7200 BC - U5b2;
4. Hohler Fels: ca. 13,400 BC - U (2 samples);
5. Hohlenstein-Stadel: 6700 BC - U5b2;

Lithuania
6. Donkalnis: Mesolithic - U5b2;
7. Spiginas: 6350 BC - U4;
9. Kretuonas: 4450 BC - U5b2; 4200 BC - U5b2;

Poland
8. Dudka: 3650 BC- U5b1 (2 samples);
10. Drestwo: 2250 BC- U5a;

Russia
11. Chekalino: 7800 BC - U5a;
12. Lebyazhinka; 8000-7000 BC - U5a1;



Map: mtDNA types from prehistoric samples of huntergatherers and farmers. The green shading represents the first farming areas (Neolithic LBK culture, 5,500-5,000 BC) in Central Europe, based on archaeological finds, while squares represent successfully analysed Late Palaeolithic, Mesolithic and Ceramist hunter-gatherers dating from 13,400BC-2300BC. The term ‘Neolithic’ is sometimes applied to the Eastern European Ceramist culture because of their use of
pottery, but this does not imply a farming economy. Previously analysed LBK farming sites are marked with circles for comparison. The area of each square or circle is proportional to the number of individuals successfully investigated.

In red are labelled archaeological sites with one or more U4/U5 individuals;
In yellow, sites with other mitochondrial DNA types

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Inferring Genealogical Processes from Patterns of Bronze-Age and Modern DNA variation in Sardinia // MBE Advance Access published online on December 2, 2009

Ghirotto et al

The ancient inhabitants of a region are often regarded as ancestral, and hence genetically related, to the modern dwellers (for instance, in studies of admixture), but so far this assumption has not been tested empirically using ancient DNA data. We studied mitochondrial DNA variation in Sardinia, across a time span of 2,500 years, comparing 23 Bronze-Age (nuragic) mitochondrial DNA sequences with those of 254 modern individuals from two regions, Ogliastra (a likely genetic isolate) and Gallura, and considering the possible impact of gene flow from mainland Italy. To understand the genealogical relationships between past and present populations we developed seven explicit demographic models; we tested whether these models can account for the levels and patterns of genetic diversity in the data, and which one does it best. Extensive simulation based on a serial coalescent algorithm allowed us to compare the posterior probability of each model and estimate the relevant evolutionary (mutation and migration rates) and demographic (effective population sizes, times since population splits) parameters, by Approximate Bayesian Computations. We then validated the analyses by investigating how well parameters estimated from the simulated data can reproduce the observed data set. We show that a direct genealogical continuity between Bronze-Age Sardinians and the current people of Ogliastra, but not Gallura, has a much higher probability than any alternative scenarios, and that genetic diversity in Gallura evolved largely independently, owing in part to gene flow from the mainland.

http://mbe.oxfordjournals.org/cgi/content/short/msp292v1

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Genetic variation in prehistoric Sardinia // Human Genetics, Volume 122, Numbers 3-4 / Ноябрь 2007 г.

Caramelli et al

Аbstract  We sampled teeth from 53 ancient Sardinian (Nuragic) individuals who lived in the Late Bronze Age and Iron Age, between 3,430 and 2,700 years ago. After eliminating the samples that, in preliminary biochemical tests, did not show a high probability to yield reproducible results, we obtained 23 sequences of the mitochondrial DNA control region, which were associated to haplogroups by comparison with a dataset of modern sequences. The Nuragic samples show a remarkably low genetic diversity, comparable to that observed in ancient Iberians, but much lower than among the Etruscans. Most of these sequences have exact matches in two modern Sardinian populations, supporting a clear genealogical continuity from the Late Bronze Age up to current times. The Nuragic populations appear to be part of a large and geographically unstructured cluster of modern European populations, thus making it difficult to infer their evolutionary relationships. However, the low levels of genetic diversity, both within and among ancient samples, as opposed to the sharp differences among modern Sardinian samples, support the hypothesis of the expansion of a small group of maternally related individuals, and of comparatively recent differentiation of the Sardinian gene pools.

http://www.springerlink.com/content/53h61344181277g3/

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A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia // Current Biology, 2010

Krause et al

]The recovery of DNA sequences from early modern humans (EMHs) could shed light on their interactions with archaic groups such as Neandertals and their relationships to current human populations. However, such experiments are highly problematic because present-day human DNA frequently contaminates bones [1,2]. For example, in a recent study of mitochondrial (mt) DNA from Neolithic European skeletons, sequence variants were only taken as authentic if they were absent or rare in the present population, whereas others had to be discounted as possible contamination [3,4]. This limits analysis to EMH individuals carrying rare sequences and thus yields a biased view of the ancient gene pool. Other approaches of identifying contaminating DNA, such as genotyping all individuals who have come into contact with a sample, restrict analyses to specimens where this is possible [5,6] and do not exclude all possible sources of contamination. By studying mtDNA in Neandertal remains, where contamination and endogenous DNA can be distinguished by sequence, we show that fragmentation patterns and nucleotide misincorporations can be used to gauge authenticity of ancient DNA sequences. We use these features to determine a complete mtDNA sequence from a ?30,000-year-old EMH from the Kostenki 14 site in Russia.

http://www.cell.com/current-biology/abstract/S0960-9822(09)02139-3

Костенки 14 (30 тыс лет) - митогаплогруппа U2
(1811-11467-12308-12372-16051)

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Genealogical Discontinuities among Etruscan, Medieval, and Contemporary Tuscans // Molecular Biology and Evolution 2009 26(9):2157-2166

Guimaraes et al

The available mitochondrial DNA (mtDNA) data do not point to clear genetic relationships between current Tuscans and the Bronze-Age inhabitants of Tuscany, the Etruscans. To understand how and when such a genetic discontinuity may have arisen, we extracted and typed the mtDNAs of 27 medieval Tuscans from an initial sample of 61, spanning a period between the 10th and 15th century AD. We then tested by serial coalescent simulation various models describing the genealogical relationships among past and current inhabitants of Tuscany, the latter including three samples (from Murlo, Volterra, and Casentino) that were recently claimed to be of Etruscan descent. Etruscans and medieval Tuscans share three mitochondrial haplotypes but fall in distinct branches of the mitochondrial genealogy in the only model that proved compatible with the data. Under that model, contemporary people of Tuscany show clear genetic relationships with Medieval people, but not with the Etruscans, along the female lines. No evidence of excess mutation was found in the Etruscan DNAs by a Bayesian test, and so there is no reason to suspect that these results are biased by systematic contamination of the ancient sequences or laboratory artefacts. Extensive demographic changes before AD 1000 are thus the simplest explanation for the differences between the contemporary and the Bronze-Age mtDNAs of Tuscany. Accordingly, genealogical continuity between ancient and modern populations of the same area does not seem a safe general assumption, but rather a hypothesis that, when possible, should be tested using ancient DNA analysis.

http://mbe.oxfordjournals.org/cgi/content/abstract/26/9/2157

Тоскана (10-15 вв)
mtDNA: H(21), T(3), K, HV