A phylogenetic analysis of the grape genus (Vitis L.): Part 2

After reading the publication A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change, I found myself in a rabbit hole, trying to understand terminology that was quite foreign to me in order to follow the conclusions contained in the article.
To aid in the determination of when and how the major branches of the genus Vitis occurred, the researchers relied on the grapevine molecular clock contained within the DNA and fossil records including:

• the oldest reliable Vitis seeds dating from the Paleocene (65.5-55.8 Ma)
• the divergence of Vitaceae and Leeaceae (stem age of Vitaceae), estimated at 90.82 – 90.65 Ma, based on a five gene data set (chloroplast rbcL, atpB,matK, and nuclear 18S and 26S nrDNA) obtained from GenBank, and conversion to absolute time using three fossil reference time points
• the divergence of the Ampelocissus-Vitis clade in the Tiffian stage of the Paleocene (62.0-56.8 Ma) based on fossil evidence
• the presence of well preserved Vitis seed at the late Neogene Gray Fossil site in Tennessee (7-4.5 Ma)

The authors used Bayesian Evolutionary Analysis by Sampling Trees (BEAST) and Randomized Accelerated Maximum Likelihood (RAxML) to report the number of unique site patterns. Based on this, they calculated that the average rate of substitution in this data set was 7.2 × 10-8 substitutions per site per million years, and used this information to calibrate the grapevine molecular clock.
The authors summarized their findings in this chronogram that shows divergence on the y-axis and geologic time line on the x-axis.¹

I used this diagram to understand the timing related to the grapevine's North American continental origin, dispersal and diversification.²

• The phylogenetic relationships and network of grapevines reflect the Northern hemisphere Cenozoic history.
• Fossil distributions suggest that, by the end of the Neogene the genus Vitis was widely distributed in the Northern Hemisphere.
• Fossils of Vitaceae have been found frequently in Western North American Eocene deposits dating from 55.8 to 33.9 Ma.
• This fossil history coupled with the DNA analysis suggest an increasing fragmentation, isolation, and differentiation beginning in North America and extending to Asia and Europe.

This origin of grapevines in North America and it's spread to Europe and Asia can be reconciled by looking at the map of Laurasia.³ During the Paleocene, the supercontinent Laurasia had only begun dividing into North America and Eurasia and the climate was much warmer. North American origin of Ampelopsis (Vitaceae), the ancestral grapevine lead to diversification in the mid-Oligocene. The rise of Vitis in the early Miocene was followed by the separation of North American and Asian land masses, In the late Miocene, this geographical separation lead to the fragmentation and speciation during the Pliocene and Pleistocene cooling cycles.
I was under the impression that the origins of the grapevine was in the Transcaucasia region, but I now know that this is related to Vitis vinifera. I now know that the ancient ancestors of that small branch of Vitis originated in North America when it was part of a supercontinent called Laurasia!
Finis!

References:
1. Yizhen Wan, Heidi R Schwaninger, Angela M Baldo, Joanne A Labate, Gan-Yuan Zhong, and Charles J Simon, A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change, BMC Evolutionary Biology 2013, 13:141.
2. SlideShare.
3. Wikipedia, Laurasia
3. Scitable, The Molecular Clock and Estimating Species Divergence.
4.Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication