Специально для русов. Гаплогруппы R1a, R1b - .......

Old World 26 analyses of the Mal’ta and Afontova Gora genomes

Posted on February 6, 2014 by Genetiker — Leave a comment

Below are the results of analyzing the Mal’ta and Afontova Gora genomes with the calculator that I used in the K = 26 admixture analysis of Amerindians and Mestizos.
The Yakut, Basque, and Sardinian components are all part Nordic, which accounts for their presence here.
The results identify the Negroid admixture appearing in the previous analyses here and here as being primarily archaic.
The largest Caucasoid or Veddoid components for the pure Amerindians in the K = 26 analysis, in decreasing order, were the Finnish, Burusho, Gujarati, and Kalash components. These components appear in the same order in the Mal’ta and Afontova Gora results, and in the Mal’ta results they even appear in approximately the same ratios as in the Amerindian results.
P* is found in South Asia, including Gujarat. Q* is found in India, Pakistan, and Afghanistan. The populations having the highest frequencies of R* are Burusho (10.3%), Kalash (6.8%), and Gujarati (3.4%).
Of all of the religions practiced today, the Kalash religion is the most similar to the original Aryan religions.
Although the Burusho language, Burushaski, is usually said to be a language isolate, there is evidence that it is related to Aryan languages.
Mal’ta

• 27.83% Finnish
• 25.95% Burusho
• 12.64% Gujarati
• 8.76% Kalash
• 5.24% Yakut
• 4.54% Brahui
• 4.10% Basque
• 2.20% Archaic
• 1.12% Papuan
• 1.10% Yoruba
• 1.06% Sardinian
• 1.03% Dai
• 0.74% San
• 0.71% Melanesian
• 0.55% Mbuti Pygmy
• 0.47% Naxi
• 0.44% Lahu
• 0.43% Biaka Pygmy
• 0.40% Mandenka
• 0.25% Kenya Bantu
• 0.20% Japanese
• 0.18% She
• 0.06% Palestinian
• 0.00% Bedouin
• 0.00% Druze
• 0.00% Mozabite

Afontova Gora

• 40.79% Finnish
• 18.33% Basque
• 14.75% Burusho
• 5.38% Gujarati
• 4.85% Kalash
• 4.12% Brahui
• 3.26% Yakut
• 2.43% Sardinian
• 1.95% Archaic
• 0.90% Melanesian
• 0.80% Yoruba
• 0.64% Papuan
• 0.48% San
• 0.44% Kenya Bantu
• 0.33% Biaka Pygmy
• 0.26% Mbuti Pygmy
• 0.17% Lahu
• 0.08% Japanese
• 0.02% Dai
• 0.01% Naxi
• 0.00% Bedouin
• 0.00% Druze
• 0.00% Mandenka
• 0.00% Mozabite
• 0.00% Palestinian
• 0.00% She
• источник

У американских эскимосов обнаружили гены пещерных людей

Фото: Stephanie Keith / Reuters

 

Гены, принадлежащие древним гоминидам, предположительно, денисовским людям, обнаружили у североамериканских эскимосов. Об этом сообщается в статье ученых, опубликованной в журнале Molecular Biology and Evolution.

След неизвестного вида человека в геномах из Южной Азии

Коренные жители Андаманских островов.

Анализ 10 полных геномов жителей Андаманских островов (к востоку от Индии) в сравнении с геномами жителей Индии привел авторов к неожиданному заключению о генетических корнях Южной и Юго-Восточной Азии. Результаты этого исследования опубликованы в журнале Nature Genetics http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3621.html.  В упомянутых геномах авторы нашли фрагменты, заимствованные от древних гоминид, которые не принадлежали ни неандертальцам, ни денисовцам. Этих фрагментов не обнаруживается в геномах ни европейцев, ни жителей Центральной и Восточной Азии.

K = 26 admixture analysis of Amerindians and Mestizos

At the bottom of this post is a K = 26 ADMIXTURE plot for HGDP and 1000 Genomes Old World populations, and ancient DNA samples. Above it is an admixture plot for HGDP and 1000 Genomes Amerindian and Mestizo populations based on results from a DIYDodecad calculator created from the ADMIXTURE analysis. Above the calculator plot are the mean admixture proportions for the Amerindian and Mestizo populations.
A while back I had done some low K ADMIXTURE analyses that included the archaic samples, and these analyses would always lump the archaics together with the Negroids. I began to suspect that the Negroid admixture showing up in analyses of ancient samples was actually archaic. This analysis confirms my suspicion. Apparently selection has weeded out a lot of archaic admixture over the past few thousand years.

Analyses of the Kostenki 14 genome

At the bottom of this post are the results of analyses of the Kostenki 14 genome. The Kostenki 14 sample is from a human skeleton that was buried at an Early Upper Paleolithic site on the west bank of the Middle Don River in Russia. The skeleton has been dated to 38,684–36,262 BP.
The mt-SNP calls for Kostenki 14 show that he belonged to mitochondrial haplogroup U2*.
The Y-SNP calls for Kostenki 14 show that he belonged to Y haplogroup C1b1-K281*. C1b1-K281 is today found primarily in South Asia, but also in Southeast Asia, the Middle East, Central Asia, and northern China.
The largest autosomal components for Kostenki 14 tended to be the North European components, which is typical for the hunter-gatherers of Upper Paleolithic and Mesolithic Europe. The second and third largest components tended to be the Veddoid South Asian or Indian components and the Caucasoid Mediterranean components, in varying order.
In this post on the Tianyuan sample I said that if we ever got 40,000-year-old DNA from Europe I expected it to show as much of the Veddoid components as Tianyuan. Kostenki 14 is pretty close to being 40,000 years old, but he had around half as much of the Veddoid components as Tianyuan. Tianyuan had 35.39% of the globe13 South Asian component, while Kostenki 14 had 16.03%. Tianyuan had 24.62% of the MDLP World-22 Indian component, while Kostenki 14 had 14.46%. This shows that Kostenki 14 was further up the path of Caucasoid evolution from Veddoids than Tianyuan was up the path of Mongoloid evolution from Veddoids.
Below are the genotypes for Kostenki 14 for SNPs that have a large effect on phenotype, with derived alleles shown in bold. Several of these results are unexpected. They show Kostenki 14 as only having one of the three Veddoid depigmentation mutations in the genes ASIP and KITLG. If the genotypes for these SNPs are correct, they suggest that there was some complexity in the distribution of these mutations in the Veddoid population before that population expanded throughout Eurasia. The results also show Kostenki 14 as having derived alleles associated with red hair, milk digestion, Mongoloid light skin, and blond hair and blue eyes.

Визуализация количества общих (IBD) сегментов у жителей Европы и Северной Азии

Originally posted by mouglley_gen at Визуализация количества общих (IBD) сегментов у жителей Европы и Северной Азии

Оригинал: Визуализация количества общих (IBD) сегментов у жителей Европы и Северной Азии

2014-07-26

Этнокалькуляторы на базе Admixture, представляющие результат «просчета» генома испытуемого в виде смеси предковых компонентов, достигли уже очень хорошей точности. Однако у них есть и определенные недостатки. Во-первых, случается, что у двух разных народов пропорции смешения этих компонентов довольно близки, хотя близкого родства между ними не наблюдается. Обычно для исключения такого эффекта увеличивают число компонентов, то есть повышают детализацию. Однако при этом зачастую возрастает и «шумность», случайные отклонения от ожидаемых значений. Кроме того, бывает тяжело понять — смешение произошло в предыдущем поколении, или тысячу лет назад? Если человек происходит из двух отдаленных народов, он часто позиционируется в географической точке, находящейся между ними, и непохож ни на один из родительских народов. При более сложносоставном происхождении все запутывается еще сильнее.

Нет ли метода напрямую измерить уровень родства отдельного человека с той или иной популяцией? При такой постановке вопроса сразу приходит на ум один из возможных ответов — необходимо просчитать количество IBD (то есть идентичных благодаря общности происхождения) аутосомных сегментов.

Инструменты и программы в генетической генеалогии

Originally posted by mouglley_gen at Инструменты и программы в генетической генеалогии

Оригинал: Инструменты и программы в генетической генеалогии

Этой заметкой мы открываем новую серию записей, в которых мы будем давать краткое описание существующих инструментов генетического генеалога.Поговорим в начале  о самых простых и самых новых инструментах.
GUI-wrapper этно-популяционного калькулятора DIY Dodecad.
http://www.y-str.org/tools/diy-dodecad-wrapper/
Многие люди жалуются на проблемы с пониманием принципов работы с калькуляторами Dienekes Dodecad, особенно что касается обработки файлов в программной среде R.  Благодаря неистощимой креативности программистов-любителей генетической генеалогии был написан wrapper (на основе платформы Microsoft.NET), позволяющий работать с калькуляторам без использования R.

Genomewide structure of populations from European Russia (Khrunin et al. 2013)

Originally posted by mouglley_gen at Genomewide structure of populations from European Russia (Khrunin et al. 2013)

Genomewide structure of populations from European Russia (Khrunin et al. 2013)

Notice:

1. The intermediate position of Estonians between Balts and Finns
2. The intermediate position of some Russian groups between Komi and the main body of Europeans.

PLoS ONE 8(3): e58552. doi:10.1371/journal.pone.0058552

A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe

Andrey V. Khrunin et al.

4-Ancestors Oracle at GEDmatch

Originally posted by mouglley_gen at 4-Ancestors Oracle at GEDmatch

posted:4-Ancestors Oracle at GEDmatch

The Jtest and EUtest at GEDmatch now include a new tool called the 4-Ancestors Oracle (aka. Oracle-4), as well as the 3D PCAs I promised earlier. Please note, Oracle-4 attempts to estimate your ethnic group of origin, and then also the most likely combinations of two, three and four ancestral populations which might have created your genome. However, this doesn't mean the results will actually show your ethnic group, or those of your parents (in dual mode) or grandparents (4-way mode). They might for many people, but for others they'll reflect the best possible outcomes from the reference samples available.

Присутствие синеглазого, светлокожего населения в раннем неолите в Иране, Армении и Леванте.

Phenotype SNPs from the ancient Near East

Below are derived allele counts and total numbers of reads for SNPs that have a large effect on phenotype for 45 genomes from the ancient Near East. Nonzero derived allele counts are in bold. Note that small derived allele counts may be due to DNA damage.
ASIP, rs2424984, Veddoid brown skin

Sample  Region   Culture            Date           D/T
I1631   Armenia  Copper Age         4250–4050 BC   1/1
I1658   Armenia  Kura-Araxes        3347–3092 BC   1/1
I1633   Armenia  Kura-Araxes        2619–2410 BC   1/1
I1635   Armenia  Kura-Araxes        2619–2465 BC   1/1
I1656   Armenia  Middle Bronze Age  1501–1402 BC   1/1
I0861   Levant   Natufian           11840–9760 BC  1/1
I1706   Levant   Early Bronze Age   2490–2300 BC   2/2
I1730   Levant   Early Bronze Age   2489–2299 BC   1/1

Присутствие светлокожего и синеглазого населения в Древнем Иране.

Phenotype SNPs from ancient Iran

Below are derived allele counts and total numbers of reads for SNPs that have a large effect on phenotype for five new ancient genomes from the Zagros Mountains of Iran. Nonzero derived allele counts are in bold. Note that small derived allele counts may be due to DNA damage.
ASIP, rs2424984, Veddoid brown skin

Sample  Period           Date BC    D/T
AH1     Early Neolithic  Unknown    3/3
AH2     Early Neolithic  8205–7756  1/1
AH4     Early Neolithic  8204–7755  0/2
WC1     Early Neolithic  7455–7082  16/16

В доколумбовой Америке встречались синеглазые и светлокожие америнды.

 В  доколумбовой  Америке  встречались  синеглазые  и  светлокожие  америнды, что  связано с  присутствием    европейских  гаплогрупп  С  и  I2.

Phenotype SNPs from the ancient Americas

 

Below are derived allele counts and total numbers of reads for SNPs that have a large effect on phenotype for ancient DNA samples from the Americas. Nonzero derived allele counts are in bold. Note that small derived allele counts may be due to DNA damage.
ASIP, rs2424984, Veddoid brown skin

Sample    Tribe    Region               Years BP   D/T
939       Unknown  British Columbia     6260–5890  2/2
MARC1492  Micmac   New Brunswick        516–258    1/1
BC25      Pericú   Baja California Sur  800–300    1/1
BC30      Pericú   Baja California Sur  800–300    2/2
MA577     Selknam  Tierra del Fuego     ~200       8/8
890       Yaghan   Tierra del Fuego     ~200       4/4
894       Yaghan   Tierra del Fuego     ~200       4/4
895       Yaghan   Tierra del Fuego     ~200       6/6

В анатолийских турках только 13% аутосом из Цетральной Азии.

Alu insertion polymorphisms and an assessment of the genetic contribution of Central Asia to Anatolia with respect to the Balkans.

 

Abstract

In the evolutionary history of modern humans, Anatolia acted as a bridge between the Caucasus, the Near East, and Europe. Because of its geographical location, Anatolia was subject to migrations from multiple different regions throughout time. The last, well-known migration was the movement of Turkic speaking, nomadic groups from Central Asia. They invaded Anatolia and then the language of the region was gradually replaced by the Turkic language.

Статуэтки белых богов из Перу.

In my White Gods post from three years ago, I included the photograph below, which shows ceramic vessels from the ancient Peruvian Moche culture (100 AD to 800 AD) that depict four obviously Caucasoid men with beards. (Note that Amerindians don’t have beards.)

Below is another ceramic vessel from the Moche culture, which portrays a European man with white skin and red hair, mustache, and goatee. The man is depicted as a prisoner bound with ropes.

Лишнее доказательство присутствия белых людей в Древнем Перу и Чили

Below is another head from the Nazca culture (100 BC to 800 AD), with fine wavy red hair.

Next are photographs of a mummy bundle of a woman from the Wari culture (500–1000 AD), which was found in 2008 in a tomb at Huaca Pucllana, an adobe brick pyramid located in the middle of the modern city of Lima. The mummy bundle was dated to around 700 AD.

Analyses of a Mesolithic genome from Karelia

Below are the results of analyses of the Mesolithic sample I0061 from Karelia, in northwestern Russia. The sample is dated to 5500–5000 BC.
I0061 belonged to Y haplogroup R1a1-M459* and mitochondrial haplogroup C1g.
globe4

• 69.18% European
• 30.82% Amerindian
• 0.00% African
• 0.00% Asian

Analyses of a hunter-gatherer genome from Samara

Below are the results of analyses of the hunter-gatherer sample I0124 from Samara, near the Volga River in Russia. The sample is dated to 5650–5555 BC.
I0124 belonged to Y haplogroup R1b1*(xR1b1a1, R1b1a2) and mitochondrial haplogroup U5a1d.
globe4

• 72.05% European
• 25.96% Amerindian
• 1.58% Asian
• 0.41% African

Путь древних этрусков в Европу

(реконструкция по аутосомным и мито-ДНК данным)
 



источник

ПИГМЕНТАЦИЯ ЕВРОПЕЙЦЕВ ЭПОХИ НЕОЛИТ

 [данные получены генетиками в результате обработки генома древних европейцев]

SHG - Scandinavian Hunter-Gatherers - Североевропейские охотники и собиратели

WHG - West-European Hunter-Gatherers - Западноевропейские охотники и собиратели

EEF - Early European Farmers - Ранние европейские земледельцы
 



источник

Денисовская примесь

А. Г. Козинцев — «Денисовская примесь обнаружена у австралийцев, папуасов, меланезийцев, негритосов маманва (Reich et al., 2011), ицзу Южного Китая (Skoglund, Jakobsson, 2011) и в некоторых группах Южной Азии (Abi-Rached et al., 2011).»
 



источник