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 Post subject: Ancient DNA Ireland (Yamnaya Ethnic Component)
 Post Posted: Tue Feb 02, 2016 12:28 am 
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Here is an extract of an journal article abstract with brief forwarded analysis as excerpted from the Cassidy (2015) et al ancient DNA study of Irish skeletal remains from Raithlin Island, notably 3 Bronze Age males (n=3) and one Neolithic female (n=1), posted on Deniekes Blog website:

“Third, we followed the methods described in Haak et al. (9), which use a collection of outgroup populations, to estimate the mixture proportions of three different sources, Linearbandkeramik (Early Neolithic; 35 ± 6%), Loschbour (WHG; 26 ± 12%), and Yamnaya (39 ± 8%), in the total Irish Bronze Age group. These three approaches give an overlapping estimate of 32% Yamnaya ancestry”.
PNAS doi: 10.1073/pnas.1518445113

Dec 29, 2015

Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome

Lara M. Cassidy, Rui Martiniano et al.

The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343–3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter–gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026–1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.
http://dienekes.blogspot.ca/

For an at(autosomal)DNA study of living British test participants and how this study may differ in certain aspects the ancient Irish DNA one highlighted above, the reader is directed to the following journal article abstract:

(http://dienekes.blogspot.ca/2015/03/bri ... -2015.html)

With regard to the above ancient DNA study note the prevalence of YDNA R1b as a founder in northern Ireland as early as app. 4042-3550 years ago. Note also the high frequency of the Yamna(ya) Western Eurasian or Eurasian Steppe at(autosomal)DNA biogeographic ethnic component in the male Ir samples, corresponding perhaps to an ancient point of origin at or near the Black-Caspian Seas (Pontic Steppe) with a migratory movement correlated to the spread of Indo-European languages (Germano-Italo-Celtic sub-families) into Western-Central Europe & the Atlantic façade (Celtiberia & British Isles) through the Balkans. Current ancient DNA, archaeogenetic or bioarchaeological research suggests that this ancient Yamna(ya) ancestral component consists of 2 subcomponents, namely EHG (Eastern Hunter Gatherer) (Balkans) + CHG (Caucasian Hunter Gatherer) (Caucasus-Central Asia-South Asia (see also the research article in Denieke’s Blog titled: Eppie R. Jones et al. (2015). Upper Palaeolithic genomes reveal deep roots of modern Eurasians, in Nature Communications 6, Article number: 8912 doi:10.1038/ncomms9912).

As a trivial side note, it seems that commercial DNA testing companies like FTDNA which offer the Family Finder atDNA test (700,000SNPs) lump the ENF (Early Neolithic Farmer/Mediterranean) & WHG (Western Hunter Gatherer) reference populations, which also includes the EHG (Eastern Hunter Gatherer)-CHG (Caucasian Hunter Gatherer) & Western Eurasian or Eurasian Steppe Yamnaya components into one cover term labelled “Western and Central European” population, without distinguishing between ENF, WHG, EHG-CHG, WHG and Yamnaya. To make a long story short, it seems that there is a continuity between ancient Irish and modern Irish atDNA and YDNA SNP. In addition there also exists a sizeable Western Eurasian or Eurasian Steppe (namely Yamnaya) ancestral component, which seems to tie into the earlier classified ANE (Ancient Northern Eurasian) ethnic component as tested in the Upper Palaeolithic Mal’ta child of Central Siberia (24,000BP). It would be interesting to see if commercial DNA testing companies like National Genographic Project incorporates these updated nomenclatures into its future database of ancient and contemporaneous population reference samples to determine and calculate ancestry informative SNP markers marking Western Eurasian or Eurasian Steppe ancestry with clear ties to South-Central Asia and the Caucasus. It would also be interesting to see the degree of continuity from ancient Irish (Ir.) DNA samples carrying the Yamnaya component (32.0%) to modern Ir. population samples. The Yamnaya biogeographic ethnic origin components as attested in the Bronze Age samples also seem to indirectly corroborate or support-however controversial or debatable-a so called “Scythian” component to the ancient Gaelic (or Goidelic) founding population that colonized Ireland-as referenced in the ancient migration myth or historical narrative titled Lebor Gabala Erenn “The Book of the Taking of Ireland” or “Book of Irish Invasions” (https://en.wikipedia.org/wiki/Lebor_Gab %C3%A1la_%C3%89renn)!


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 Post subject: Re: Ancient DNA Ireland (Yamnaya Ethnic Component)
 Post Posted: Tue Feb 16, 2016 12:34 am 
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All commercial DNA testing companies such as Ancestry.ca, National Genographic (Geno 2.0), FTDNA Family Finder and 23andMe fail to differentiate the so called Yamnaya (West Eurasian Steppe) ancestral component as a reference population sample to reflect changes in recentaDNA research, where the aDNA samples from Ireland show 37.0% +/ -8.0% (47-31%)Russian Euarsian Steppe (North of Black & Caspian Sea) ancient ethnic origin component. Although recent studies conducted among living Irish-Scots Gaelic descendants, one would expect an app. estimate of 31.0-32.0% Steppe ancestry. It seems that National Genographic Geno 2.0 lumps the Yamnaya component in the Northern European reference population. Furthermore, it seems that unlike FTDNA which distinguishes Western-Central European, Finnish or Northern Siberian, as well as a Scandinavian components, Nat Geno lumps all these in either of the Northern European or Mediterranean ones.

Nat Geno defines the three principal components of British Isles or United Kingdom (Anglo-Saxon & Brythonic-Goidelic Celtic) as follows:

Northern European: This component is found at highest frequency in northern European populations—people from the UK, Denmark, Finland, Russia and Germany in our reference populations. While not limited to these groups, it is found at lower frequencies throughout the rest of Europe. This component is likely the signal of the earliest hunter-gatherer inhabitants of Europe, who were the last to make the transition to agriculture as it moved in from the Middle East during the Neolithic period around 8,000 years ago.

Mediterranean: This component is found at highest frequencies in southern Europe and the Levant—people from Sardinia, Italy, Greece, Lebanon, Egypt and Tunisia in our reference populations. While not limited to these groups, it is found at lower frequencies throughout the rest of Europe, the Middle East, Central and South Asia, due to these populations traveling through this region on their journeys and retaining that in their DNA. This component is likely the signal of the Neolithic population expansion from the Middle East, beginning around 8,000 years ago, likely from the western part of the Fertile Crescent.

Southwest Asian: This component is found at highest frequencies in India and neighboring populations, including Tajikistan and Iran in our reference dataset. It is also found at lower frequencies in Europe and North Africa. As with the Mediterranean component, it was likely spread during the Neolithic expansion, perhaps from the eastern part of the Fertile Crescent. Individuals with heavy European influence in their ancestry will show traces of this because all Europeans have mixed with people from Southwest Asia over tens of thousands of years.
(https://genographic.nationalgeographic.com/regions/" onclick="window.open(this.href);return false;)

Nat Geno approximates the average UK British test participant atDNA ancestral components as follows:

BRITISH (UNITED KINGDOM)

This reference population is based on samples collected from populations in the United Kingdom. The dominant 50% northern European component likely reflects the earliest settlers in Europe, hunter-gatherers who arrived there more than 35,000 years ago. The 33% Mediterranean and 17% Southwest Asian percentages arrived later, with the spread of agriculture from the Fertile Crescent in the Middle East, over the past 10,000 years. As these early farmers moved into Europe, they spread their genetic patterns as well. Today, northern European populations retain their links to both the earliest Europeans and these later migrants from the Middle East.

(https://genographic.nationalgeographic. ... pulations/" onclick="window.open(this.href);return false;)

Note that Yamnaya, contains in addition to EHG and CHG, an ANE (Ancient North Eurasian) component, as adetected in an acient Upper Paleolithic mammoth hunter skeleton excavated from Mal`ta (Lake Baikal, Central Siberia), dated ca. 24,000BP, having atDNA shared with Eurasian hunter-gatherers as well as some Native American groups. Deniekes Blog commentary suimmarizes the research paper analysis results and abstract as follows (excerpted):

The study I mentioned in a previous post has now been made available in Nature. Two Upper Paleolithic Siberians (24-17kya) have been sequenced at low coverage. The better quality (and older) Mal'ta (MA-1) sample belongs to Y-haplogroup R and mtDNA haplogroup U, and the younger (but poorer quality) Afontova Gora (AG-2) sample appears to be related to it.

Most interestingly, there is evidence for gene flow between the MA-1 sample and Native Americans, which makes sense as these are Siberians of the period leading up to the initial colonization of the Americas. The interesting thing is that MA-1 does not appear to be East Eurasian, as proven by the test D(Papuan, Han; Sardinian, MA-1) which is non-significant, so MA-1 is not more closely related to Han than to Papuans (which is true for modern native Americans). So, it seems that the gene flow between MA-1 and Native Americans was towards Native Americans from MA-1 and not vice versa.

It is fascinating that such a sample could be found so far east at so early a time. Both Y-chromosome R and mtDNA haplogroup U are very rare east of Lake Baikal which has been considered a limit of west Eurasian influence into east Eurasia. And, indeed, both these haplogroups are absent in Native Americans, so it is not yet clear how Native Americans (who belong to Y-chromosome haplogroups Q and C and mtDNA haplogroups A, B, C, D, X) are related to these Paleolithic Siberians. The obvious candidate for this relationship is Y-chromosome haplogroup P (the ancestor of Q and R). So, perhaps Q-bearing relatives of the R-bearing Mal'ta population settled the Americas.

In any case, this is an extremely important sample, as its position in "no man's land" in the PCA plot (left) demonstrates, between Europeans and native Americans but close to no modern population.

Its closest present-day relatives are indicated in (c), with Native Americans (red) being the closest, and a scattering of boreal populations from the Atlantic to the Pacific (but not in the vicinity of Lake Baikal) next in line (yellow).

This distribution clearly related to the evidence for admixture in Europe adduced in two other recent papers, although the question of who went where and when remains to be resolved. Was MA-1 part of an intrusive western population encroaching on east Eurasians? Or did MA-1 lookalikes arrive as first settlers in empty territory, later ceding this space to east Eurasians from, perhaps, China? Did the two mix in Siberia or did they arrive in the Americas in separate migrations and mix there? And, how does this all relate to events in Europe in the far west?

End of Excerpt

(http://dienekes.blogspot.ca/2013/11/anc ... -lake.html" onclick="window.open(this.href);return false;)

Abstract: (as excerpted)

Nature (2013) doi:10.1038/nature12736

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

Maanasa Raghavan, Pontus Skoglund et al.

The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians1, 2, 3, there is no consensus with regard to which specific Old World populations they are closest to4, 5, 6, 7, 8. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal’ta in south-central Siberia9, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers10, 11, 12, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages5. Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians2, 13. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago14, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.

(End of Abstract)

http://dienekes.blogspot.ca/2013/11/anc ... -lake.html

So it does seem that Western Europeans who trace ancestry back to the Yamnaya Steppe herders, via ancient ancestry to the Upper Paleolithic Mal`ta-Afontova Gora groups, also descend from the same ancient basal group that had contact through intermarriage-perhaps with unidirectional asymmetric or skewed gene flow from Upper Paleolithic Eurasian to the ancestors of Beringian Standstill Paleoindians after their divergence from East Asian-Northeast Asian or Beringian Siberian, prior to migrating to the New World. Note also the recent discovery of 3 out 55 haplogroup M (attested in Asian, Australasian and Native American groups) (root of mtDNA haplogroups A, B, C, D) mtDNA haplogroups sequenced from aDNA specimens excavated from prior LGM (Last Glacial Maximum) (35,000BP) sites in Western Europe, showing that not was West Eurasian YDNA haplogroup R (son of paragroup P-M45, & brother of Q) extended further east into Eastern Eurasia-Siberia, but mtDNA M extended further west into the Atlantic facade or coastal fringe of the Iberian peninsula-perhaps, although controversially given some credence to the plausibility of ancient pre-Solutrean groups migrating across the Atlantic Ocean, colonizing Eastern North America! The geographic distribution of the above YDNA and mtDNA haplogroups coincide with an ancient migration route or corridor of UP hunter-gatherers extending from Iberia to Lake Baikal, through the Russian Steppe into the Pleistocene and up until the immigration of Yamnaya kin groups, presumably carrying Indo-European languages, culture and genetics from the Eurasian Russian Steppes north of the Black-Caspian Seas, during the Bronze Age.


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 Post subject: Re: Ancient DNA Ireland (Yamnaya Ethnic Component)
 Post Posted: Thu Jan 26, 2017 11:51 pm 
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Here is a breakdown of the estimated bio-geographic ethnic origin percentages of Yamnaya, Bell Beaker and CWC (Corded Ware Culture) ancient atDNA whole genome sequences currently held in the DNALand (https://dna.land/) database, as calculated from that company`s propietary aDNA reference population database and algorithmic calculators:

I. West Eurasia (Black-Caspian Seas westward to NW-NE Europe, including Balkans, Mediterranean & North Africa):

i.) Yamnaya Culture (Sample I0433), Sok River

West Eurasian 100.0% (NW Europe 42.0%; NE Europe 40.0% (North Slavic 36.0%, Finland 3.5%); Central Asian 18.0% (Indus Valley 12.0%, Kalash 5.5%))

NOTE: It is interesting that DNALand lumps Central Asian under West Eurasian given the known overlapping inputs from East Asian and South Asian (Ancient North and South Asian). Note that the average NW European such as Goidelic-Brythonic Celts from the British Isles shows app. 15-20% Yamnaya Eurasian (Black-Caspian Sea) Steppe (a proxy for ANE-Ancient North Eurasian) (or what National Genographic calls SW Asian).

ii.) CWC (Corded Ware Culture) (Sample I0104), Esperstedt, Germany

West Eurasian 100.0% (NW Europe 69.0%; NE Europe 26.0% (North Slavic 22.0%, Finland 4.5%); Central Asian 5.2% (Kalash 4.0%, Indus Valley 1.2%))

NOTE: The North Slavic (NE European) component-also somehow interconnected with East Europe & Finland-NW Russia also shows up at low frequencies among several Paleoamerican or Paleoindian skeletal, such as Kennewick Man and Anzick-1. This component may also be a reflex or residue of the ANE component in West Eurasia and West-Central Siberia.

iii.) Corded Ware woman, Oblaczkowo, Poland

West Eurasian 100.0% (North Slavic 84.0%; NW Europe 10.0%; Sardinian 5.7%)

iv.) Bell Beaker woman (Sample I0112), Quedlinburg, Germany

West Eurasian 100.0% (NW Europe 74.0%; North Slavic 22.0%; SW Europe 4.1%)

v.) Bell Beaker-Corded Ware (Sample I0118), Alberstedt, Germany (2471-2246 BC)

West Eurasian 100.0% (NW European 65.0%; North Slavic 17.0%; SW Europe 16.0% (SW Europe 15.0, Sardinian 1.4%); Mediterrean Islander 1.2%; Balkan 1.1%)

vi.) Ireland Neolithic (Ballynahatty)

SW Europe 100.0% (Sardinia 56.0%, SW Europe 44.0%)

vii.) Villabruna (UP-Upper Paleolithic Europe, Italy, ca. 14,000 BP)

West Eurasian 100.0% (NE Europe 77.0% (North Slavic 62.0%, Finland 15.0%); NW Europe 21.0%; SW Europe 1.8%)

NOTE: It is interesting that Villabruna (one of the oldest attested samples bearing NR-YHg R1b in Western Europe) also has a high North Slavic component, while other whole genomic studies (Eurogenes Ancestry Project) suggest a strong SW Asia (West Asia or Asia Minor) and Levantine-Mediterranean component.

viii.) RISE 98, Battle Axe Man, Little Beddinge, Ssweden

West Eurasian 99.0% (NW Europe 50.0%, NE Europe 46.0% (North Slavic 43.0%, Finland 2.5%); Sardinia 2.9%; Ambiguous 1.0%)

ix.) RISE 598 Turlojiske, Lithuania-Poland border, Bronze Age

North Slavic 100.0%

x.) RISE 145 Bronze Age Unetice, Polwica, W Poland

West Eurasian 96.0% (North Slavic 56.0%; NW Europe 18.0%; Balkan 14.0%; Sardinia 5.6%; Kalash 2.8%)
Hadza 1.5%
Ambiguous 1.4%
Native American 1.2%
Ambiguous 1.2%

NOTE: A NA-Native American component is detected in this ancient sample.

xi.) Karelia I0061

NE European 87.0% (North Slavic 59.0%, Finland 28.0%)
Native American 12.0% (Native American 8.7%, 2.8%)
Tubular 1.5%

NOTE: A relatively strong NA-Siberian (13.5%) component is detected suggesting that residual traces of this ANE (AG-Malta) component survived in NE Europe (NW Russia-Baltics).

xii.) NG21-10 Serbia 6600 BP

West Eurasia 100.0% (Sardinia 66.0%; Balkan 34.0%)

xiii.) Chalcolithic El Mirador, Spain

SW Europe 100.0% (Sardinia 61.0%, SW Europe 39.0%)

xiv.) Oase Pestera cu Oase Romania (40,000 BP)

West Eurasian 56.0% (South Asian 32.0% (Dravidian 30.0%, Gujarati 2.9%); Mediterranean Islander 15.0%, NW Europe 5.0%; Finland 3.2%; Ambiguous 1.1%)
Cambodian (Thai) 18.0%
African 17.0% (East Africa 7.1% (4.1%, Hadza 3.0%); South African 4.4%; Aka 4.0%; Ambiguous 1.0%)
North Oceanic 9.1%

NOTE: A combined SE Asian (27.1%) component existed in SE Europe (Balkans) during the UP (Upper Paleolithic). Interestingly, a high South Asian (32.0%) component is also present!

II. West & Central Siberia (including Volga & Ural regions):

Kostenki 14 South Russia 40,000 BP

i.) West Eurasian 79.0% (SW Europe 35.0%; North Slavic 19.0%; Dravidian 11.0%; Central Asian 11.0% (Indo-Iranian 4.7%, Indus Valley 4.7%, Mid-Tushi 2.8%); Ambiguous 1.6%; NW Europe 1.3%)
Native Oceania 6.5%
Africa 6.2% (South Africa 2.5%, Aka 2.2%, North Africa 1.5%)
Amazon 4.5%
Tubular 3.6%

NOTE: According to Max Planck Institute reports Kostenki 14 shows the closest genomic affinity to most living West Eurasians (NW & NE Europeans). Note also the relatively high SE Asian (6.5%) & NA-Siberian (8.1%) bio-geographic ethnic origin percentages.

ii.) Khvalynsk (I0122), Volga Region

West Eurasian 94.0% (NE Europe 81.0% (North Slavic 75.0%, Finland 6.0%); NW Europe 8.8%; Central Asia 5.0% (Kalash 3.9%, Indus Valley 1.1%)
Native American 5.6% (Native American 3.7%, Amazonian 1.8%)

NOTE: The Volga River West Siberian groups like the Samara one below show relatively high NA percentages-the same argument can be extended for the Okunevo-Karasuk cultural complexes of West Siberia. This may also explain why app. 1.0-3.0% NA bio-geographic ethnic origin percentages show for some German test participants through crowd-sourced, direct-to-consumer, commercial, genetic genealogy testing companies.

iii.) Samara Oblast Sok River EHG (Eastern Hunter Gatherer) (I0124) (5650-5555 BC)

NE Europe 92.0% (North Slavic 69.0%, Finland 23.0%)
Native American 7.8%

III. East Eurasian:

i.) Tianyuan Cave man 40,000 BP

East Asia 59.0% (East Turkic 3.5%; NE Asian 18.0% (Siberian 9.5%, Tubular 8.7%); Cambodian-Thai 5.9%
West Eurasian 30.0% (North Slavic 27.0%, Gujarati 3.8%)
Native American 4.0%
Native Oceanic 3.6%
Ambiguous 2.7%

NOTE: A relatively high West Eurasian bio-geographic ethnic component is recorded for this sample, perhaps suggestive of an ancient link between Central-South (Altaic) Siberian Caucasoid group and ANE-Malta groups ancestral to Native Americans.

IV.) Native American (New World Amerindian):

i.) Precolumbia Peru (NA41) (Chachapoyas or Inca)

Native American 91.0% (Native American 77.0%, Amazonian 13.0%)
Hadza 4.3%
Kalash 3.3%
Siberian 1.8%

NOTE: The 4.3% Hadza African component may be a signal from distant or remote Denisovan (100.0% African) ancestry detected in many Central-South Amerindian (Andean) groups.

V.) Archaic Hominids:

i.) Altai Neanderthal:

Africa 100.0% (South Africa 65.0%; Pygmy 35.0% (Aka 25.0%, Mbuti 10.0%)

NOTE: According to National Genographic Project the average NW European (West Eurasian) shows around 1.0-3.0% Neanderthal atDNA. If so, then by logical reasoning would this not imply that the average NW European also has around 1.0-3.0% African atDNA-as per other genomic studies which show the survival of a low level SSA (Sub-Saharan African) trace in groups such as the Goidelic Celts (Irish Gaels)!

ii.) Denisova Cave:

Africa 100.0% (South Africa 50.0%; Pygmy 50.0% (Aka 34.0%, Mbuti 16.0%))

Disclaimer: some of the estimated bio-geographic ethnic percentages as calculated through the algorithm calculator- for some reason or another-do not consistently add up to even whole numbers, and as ushc may be off by app. 0.5% points.

For any reader interested in furthering their knowledge of European a(ancient)DNA the following blog websites are highly recommended: http://eurogenes.blogspot.ca/
http://bellbeakerblogger.blogspot.ca/; & http://forwhattheywereweare.blogspot.ca/


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