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Jean M
06-26-2016, 01:30 AM
Nathan Wales et al., The limits and potential of paleogenomic techniques for reconstructing grapevine domestication, Journal of Archaeological Science, Volume 72, August 2016, Pages 57–70 http://www.sciencedirect.com/science/article/pii/S0305440316300772


In ancient DNA (aDNA) research, evolutionary and archaeological questions are often investigated using the genomic sequences of organelles: mitochondrial and chloroplast DNA. Organellar genomes are found in multiple copies per living cell, increasing their chance of recovery from archaeological samples, and are inherited from one parent without genetic recombination, simplifying analyses. While mitochondrial genomes have played a key role in many mammalian aDNA projects, including research focused on prehistoric humans and extinct hominins, it is unclear how useful plant chloroplast genomes (plastomes) may be at elucidating questions related to plant evolution, crop domestication, and the prehistoric movement of botanical products through trade and migration. Such analyses are particularly challenging for plant species whose genomes have highly repetitive sequences and that undergo frequent genomic reorganization, notably species with high retrotransposon activity. To address this question, we explored the research potential of the grape (Vitis vinifera L.) plastome using targeted-enrichment methods and high-throughput DNA sequencing on a collection of archaeological grape pip and vine specimens from sites across Eurasia dating ca. 4000 BCE–1500 CE. We demonstrate that due to unprecedented numbers of sequence insertions into the nuclear and mitochondrial genomes, the grape plastome provides limited intraspecific phylogenetic resolution. Nonetheless, we were able to assign archaeological specimens in the Italian peninsula, Sardinia, UK, and Armenia from pre-Roman to medieval times as belonging to all three major chlorotypes A, C, and D found in modern varieties of Western Europe. Analysis of nuclear genomic DNA from these samples reveals a much greater potential for understanding ancient viticulture, including domestication events, genetic introgression from local wild populations, and the origins and histories of varietal lineages.

Saetro
06-26-2016, 01:59 AM
Interested in what else could be out there on this topic? Here is one other example, unfortunately also behind a pay wall, apart from its abstract.

Multiple origins of cultivated grapevine (Vitis vinifera L. ssp. sativa) based on chloroplast DNA polymorphisms, by R. ARROYO-GARCÍA et al (2006)
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2006.03049.x/full
The domestication of the Eurasian grape (Vitis vinifera ssp. sativa) from its wild ancestor (Vitis vinifera ssp. sylvestris) has long been claimed to have occurred in Transcaucasia where its greatest genetic diversity is found and where very early archaeological evidence, including grape pips and artefacts of a ‘wine culture’, have been excavated. Whether from Transcaucasia or the nearby Taurus or Zagros Mountains, it is hypothesized that this wine culture spread southwards and eventually westwards around the Mediterranean basin, together with the transplantation of cultivated grape cuttings. However, the existence of morphological differentiation between cultivars from eastern and western ends of the modern distribution of the Eurasian grape suggests the existence of different genetic contribution from local sylvestris populations or multilocal selection and domestication of sylvestris genotypes. To tackle this issue, we analysed chlorotype variation and distribution in 1201 samples of sylvestris and sativa genotypes from the whole area of the species’ distribution and studied their genetic relationships. The results suggest the existence of at least two important origins for the cultivated germplasm, one in the Near East and another in the western Mediterranean region, the latter of which gave rise to many of the current Western European cultivars. Indeed, over 70% of the Iberian Peninsula cultivars display chlorotypes that are only compatible with their having derived from western sylvestris populations.

Jean M
06-26-2016, 10:08 AM
Interested in what else could be out there on this topic? Here is one other example, unfortunately also behind a pay wall, apart from its abstract.

The lead author has made the paper available in full via https://www.researchgate.net/ and also in pdf from https://www.ars.usda.gov . Just Google on the title.

Jean M
06-26-2016, 10:33 AM
More recent is the paper Myles, S. et al. 2011. Genetic structure and domestication history of the grape, PNAS, 108 (9), 3530–3535. http://www.pnas.org/content/108/9/3530.abstract


The grape is one of the earliest domesticated fruit crops and, since antiquity, it has been widely cultivated and prized for its fruit and wine. Here, we characterize genome-wide patterns of genetic variation in over 1,000 samples of the domesticated grape, Vitis vinifera subsp. vinifera, and its wild relative, V. vinifera subsp. sylvestris from the US Department of Agriculture grape germplasm collection. We find support for a Near East origin of vinifera and present evidence of introgression from local sylvestris as the grape moved into Europe. High levels of genetic diversity and rapid linkage disequilibrium (LD) decay have been maintained in vinifera, which is consistent with a weak domestication bottleneck followed by thousands of years of widespread vegetative propagation. The considerable genetic diversity within vinifera, however, is contained within a complex network of close pedigree relationships that has been generated by crosses among elite cultivars. We show that first-degree relationships are rare between wine and table grapes and among grapes from geographically distant regions. Our results suggest that although substantial genetic diversity has been maintained in the grape subsequent to domestication, there has been a limited exploration of this diversity. We propose that the adoption of vegetative propagation was a double-edged sword: Although it provided a benefit by ensuring true breeding cultivars, it also discouraged the generation of unique cultivars through crosses. The grape currently faces severe pathogen pressures, and the long-term sustainability of the grape and wine industries will rely on the exploitation of the grape's tremendous natural genetic diversity.

That is the one I cite in AJ. I am not sure that the paper I reported in the OP is getting us a lot further, but it seemed worth mentioning.

razyn
06-26-2016, 02:07 PM
I had attempted to raise this topic in a 2014 thread here http://www.anthrogenica.com/showthread.php?2711-Does-the-connection-of-M269-with-copper-skills-go-right-back-to-its-invention&p=44053&viewfull=1#post44053, after which I swapped several emails with Patrick E. McGovern at Penn. His 2006 book Ancient Wine is well known, but far from the last word he has uttered on the subject. Here is an informal update from 2015: http://www.penn.museum/sites/biomoleculararchaeology/?p=1913

I'm pleased to see Jean's link (in the OP here) to a paper dated two months in the future. Not that I understand chloroplast genomics, at all -- but somebody is at least looking. The last sentence of this new abstract (I'll quote it below) is reminiscent of the propaganda we were seeing for NextGen sequencing of human nuclear DNA, just a couple of years ago; and that optimism has turned out to have been largely correct -- if anything, understated.


Analysis of nuclear genomic DNA from these samples reveals a much greater potential for understanding ancient viticulture, including domestication events, genetic introgression from local wild populations, and the origins and histories of varietal lineages.

Saetro
06-26-2016, 08:59 PM
The lead author has made the paper available in full via https://www.researchgate.net/ and also in pdf from https://www.ars.usda.gov . Just Google on the title.

I usually find Google Scholar brings up these accessible equivalents, but not in this case.
I will need to broaden my search techniques in future.

J Man
07-04-2016, 06:09 PM
I remember reading before that Georgia in the South Caucasus is thought to be an area of very early grape cultivation and wine making as well.

Jean M
07-04-2016, 06:22 PM
I remember reading before that Georgia in the South Caucasus is thought to be an area of very early grape cultivation and wine making as well.

I go for the South Caucasus in AJ:


Grapes grew wild on the southern shores of the Black and Caspian Seas, climbing trees like lianas. They seem to have been first cultivated on the sunny southern slopes of the Caucasus.[McGovern 2003 and 2009.] The earliest complete winery was found in a cave in southern Armenia, close to Iran, complete with press, fermentation vats and storage jars. The species of grape was confirmed to be the domesticated variety. The complex has been radiocarbon-dated to 4100-4000 BC.[Barnard 2011.] A genetic study of varieties of grape vine supports an origin of grape domestication in the Near East.[Myles 2011.]

Volat
07-04-2016, 09:20 PM
Georgia is often mentioned as the region of grape domestication and earliest wine-making. Georgia keeps their traditional wine making having unique grape variety aging their wines in clay vessels known as Kvevri. Europeans age their red wines in oak barrels.

Georgian Kveri https://en.wikipedia.org/wiki/Kvevri


http://media.npr.org/assets/img/2015/06/08/qvevri_custom-864aff8ef8add761de0f65aafc11125597f75148-s800-c85.jpg

razyn
07-11-2016, 09:19 PM
I just ran across a 2012 lecture by Patrick McGovern (mentioned previously in this thread) that looks promising. Will watch it in the next few days, if not hours. I have enjoyed two of his books, so I expect it will be both informative and kind of droll. https://www.youtube.com/watch?v=8K4Avq751ts

Edit: Having now viewed it, I recommend it highly. At the end there's a link to a 2013 lecture, that I have not watched. But since I can still link it in the same post, I shall: https://www.youtube.com/watch?v=4eYztv0ZAEQ#t=0.232208

Heber
09-11-2016, 04:06 AM
Georgia is often mentioned as the region of grape domestication and earliest wine-making. Georgia keeps their traditional wine making having unique grape variety aging their wines in clay vessels known as Kvevri. Europeans age their red wines in oak barrels.

Georgian Kveri https://en.wikipedia.org/wiki/Kvevri


http://media.npr.org/assets/img/2015/06/08/qvevri_custom-864aff8ef8add761de0f65aafc11125597f75148-s800-c85.jpg

I would love to get aDNA from this culture and from these wine residues and prehistoric grape pips.

"Jalabadze is talking about a Neolithic culture called Shulaveri-Shomu whose mound sites in Georgia arose during a wet cycle in the southern Caucasus and date back to first inklings of agriculture, before the time of metal. The villagers used stone tools, tools of bone. They crafted gigantic pots the size of refrigerators. Such vessels—precursors to the fabled kvevri—held grains and honey, but also wine. How can we know? One such pot is decorated with bunches of grapes. Biochemical analyses of the pottery, carried out by McGovern, shows evidence of tartaric acid, a telltale clue of grape brewing. These artifacts are 8,000 years old. Georgia’s winemaking heritage predates other ancient wine-related finds in Armenia and Iran by centuries. This year, researchers are combing Shulaveri-Shomu sites for prehistoric grape pips......

“Typical human migrations involved mass slaughter,” says Stephen Batiuk, an archaeologist at the University of Toronto. “You know, migration by the sword. Population replacement. But not the people who brought wine culture with them. They spread out and then lived side-by-side with host cultures. They established symbiotic relationships.”

http://nationalgeographic.org/projects/out-of-eden-walk/articles/2015-04-ghost-of-the-vine/

It may explain the success of cultures like Bell Beaker and the significance of the Beaker itself.

http://blogs.sapo.pt/cloud/file/eb6b52b82097d41dfa0e5797a2fa7945/olympusmons/2016/From%20Shulaveri%20to%20Bell%20beaker.pdf

Volat
09-11-2016, 06:25 AM
I don't care about their aDNA. Some red Georgian wines are delicious. Highly praised by people who love red wines. Georgian best wines don't cost a leg and an arm as famous French wines.

Heber
09-17-2016, 07:38 PM
It’s uncertain where, exactly, viticulture began, but the strongest theories suggest that it arose between the Black and Caspian Seas in Transcaucasia (which includes Armenia, Georgia, and Azerbaijan), as well as in eastern Turkey, the Levant, and northern Iran. The earliest evidence for grape domestication, in the form of 8,000-year-old grape seeds, was found just north of Armenia at Shulaveri gorge in Georgia. The oldest example of wine—7,400-year-old residue on clay pots—was discovered just south of Armenia at Hajji Firuz Tepe in Iran. Across the Black Sea in northern Greece, findings from a settlement called Dikili Tash suggest that grapes were being crushed into wine there 6,300 years ago. But Areni-1, at 6,100 years old, is the first place where grapes and winemaking tools have been discovered together. To put things in perspective, it’s not until a millennium or so later that wine shows up in the tombs of Egyptian pharaohs.

http://www.saveur.com/world-oldest-winery-armenia

http://www.peopleofar.com/2014/12/17/10-worlds-oldest-things-from-armenia/

11696

11697

The Kura Araxes is also where R1b aDNA was found in the latest Lazaridis paper.

http://www.pnas.org/content/112/30/9190.abstract

11698

And it is on the route from Kura Araxes, Kuban, Azov, Maikop, Yamnaya, Corded Ware and could be the source of the missing R1b- L51 branch.

11699

The Caucasus sits on the crossroads of the Eurasian land mass and we can expect more revealing aDNA from this region.

Heber
10-18-2016, 12:04 PM
Genomics breakthrough paves way for climate-tolerant wine grape varieties
October 17, 2016

A new sequencing technology, combined with a new computer algorithm that can yield detailed information about complex genomes of various organisms, has been used to produce a high-quality draft genome sequence of cabernet sauvignon, the world's most popular red wine grape variety, reports a UC Davis genomics expert.

Read more at: http://phys.org/news/2016-10-genomics-breakthrough-paves-climate-tolerant-wine.html#jCp

http://phys.org/news/2016-10-genomics-breakthrough-paves-climate-tolerant-wine.html

Jean M
11-06-2016, 10:10 PM
I have only just seen http://www.wineofancientegypt.com/

There is a book chapter on the project too: Maria Rosa Guasch-Jané, An Interdisciplinary Study on the Ancient Egyptian Wines: The Egywine Project, Digital Heritage. Progress in Cultural Heritage: Documentation, Preservation, and Protection, Volume 10058 of the series Lecture Notes in Computer Science pp 737-748.


This article presents the research results of the ‘Irep en Kemet’ Project that studies the Ancient Egyptian wine culture and the newly developed website of the research project [www.​wineofancientegy​pt.​com] to transfer the knowledge and disseminate the results. For the first time, the corpus of the viticulture and winemaking scenes in the ancient Egyptian private tombs has been developed, together with the bibliographical and scene-detail databases. The second phase of the ‘Irep en Kemet’ website includes an interactive archaeological map of Egypt with the viticulture and winemaking scenes, and also the databases and the results of the research. Moreover, the objectives and preliminary results of the EGYWINE project that investigates the wine jars and wine inscriptions, and the ancient DNA of the Egyptian wines, are presented.

http://link.springer.com/chapter/10.1007/978-3-319-48496-9_59

Jean M
08-30-2017, 07:49 AM
https://www.sciencedaily.com/releases/2017/08/170824141201.htm

World's oldest Italian wine just discovered: Ancient pottery tests positive for wine

Italian wine residue has been found from the Copper Age, debunking current belief wine growing and wine production in Italy developed during the Middle Bronze Age.


Chemical analysis conducted on ancient pottery could dramatically predate the commencement of winemaking in Italy. A large storage jar from the Copper Age (early 4th millennium BC) tests positive for wine. This finding published in Microchemical Journal is significant as it's the earliest discovery of wine residue in the entire prehistory of the Italian peninsula. Traditionally, it's been believed wine growing and wine production developed in Italy in the Middle Bronze Age (1300-1100 B.C.) as attested just by the retrieval of seeds, providing a new perspective on the economy of that ancient society.

Actual paper: Davide Tanasi, Enrico Greco, Valeria Di Tullio, Donatella Capitani, Domenica Gullì, Enrico Ciliberto. 1 H- 1 H NMR 2D-TOCSY, ATR FT-IR and SEM-EDX for the identification of organic residues on Sicilian prehistoric pottery. Microchemical Journal, 2017; DOI: 10.1016/j.microc.2017.08.010

razyn
08-30-2017, 10:09 PM
I haven't read the paper, but the quotation doesn't make it obvious to me that this wine, of which a residue has been found in an ancient storage jar in present Italy, was from locally grown grapes (or was locally fermented). Could have been imported; could previously have been in skins. From somewhere, a boat ride distant from Italy.


A large storage jar from the Copper Age (early 4th millennium BC) tests positive for wine. This finding published in Microchemical Journal is significant as it's the earliest discovery of wine residue in the entire prehistory of the Italian peninsula. Traditionally, it's been believed wine growing and wine production developed in Italy in the Middle Bronze Age (1300-1100 B.C.)

OTOH it's a pretty good argument, as stated, against the prevailing wisdom that Bell Beakers were necessarily for drinking something like beer or mead [because wine was supposed to be unknown in the region as early as the Bell Beaker era]. This storage jar is about a thousand years older than the Beaker era.

Volat
12-03-2017, 10:12 AM
Georgian wine is the oldest (8,000 ybp) as per Guinness Book of records. The entry about Georgian wine being the oldest was made recently : http://www.guinnessworldrecords.com/world-records/68379-oldest-wine





Chemical evidence of wine, dating back to 6000–5800 BC (the early Neolithic period), was obtained from residues of ancient pottery excavated in the archeological sites of Gadachrili Gora and Shulaveris Gora, about 50 km south of Tbilisi in Georgia. The residues were identified as wine since they contained tartaric acid, which only occurs in large amounts in the Eurasian grape (Vitis vinifera) in the Middle East and the wine made from it. The detection of other organic acids (malic, citric and succinic), also found in the Eurasian grape, provided confirmatory evidence.

The wine residues were recovered from large-capacity jars, which were probably used for fermentation, ageing and storage. Prior to this discovery, the oldest chemically identified wine from Hajji Firuz Tepe (Iran) dated back to about 5400–5000 BC. These new findings are from about 600–1,000 years earlier, and indicate that wine-making and possibly viticulture were already in place about 8,000 years ago.

The discovery was made by Prof. Patrick McGovern, a molecular archaeologist from the University of Pennsylvania Museum of Archaeology and Anthropology and lead author of the study "Early Neolithic Wine of Georgia in the South Caucasus", published online in the journal Proceedings of the National Academy of Sciences (PNAS) on 13 November 2017, and scientists from institutions in Georgia, France, Italy, Israel, Canada, Denmark and the USA, who participated in the joint “Research Project for the Study of Georgian Grapes and Wine Culture".