A phylogenetic analysis of the grape genus (Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change

Table 1 Comparison of divergence estimates in Vitis among five studies that analyzed SNP data and used zero, two or three fossil calibration points

Node¹	Xiang et al. 2000²[55]	Nie et al. 2010³[34]	Zecca et al. 2012^4,5[36]	Liu et al. 2013⁶[35]	Present study⁷
Vitis crown
Estimate (Ma)	_⁸	~8	18.60, 19.05⁵	~12	28.32
95% HPD (Ma)	_	~16-4	28.79-9.50, 29.07-10.2	~22-6	41.25-16.23
subg. Vitis crown
Estimate (Ma)	_	~5.5	6.31, 6.55	~7	17.82
95% HPD (Ma)	_	~10-2.5	9.50-3.50, 9.34-4.50	~11-5	26.71-10.14
Europe/Near East - Asia
Estimate (Ma)	_	_	4.31, 4.47	_	6.36
95% HPD (Ma)	_	_	6.60-2.31, 6.71-2.61	_	9.80-3.36
Eurasia-NC America
Estimate (Ma)	4.98 (5.98- < 0.28)	_	6.31, 6.55	_	11.12
95% HPD (Ma)	_	_	9.50-3.50, 9.34-4.50	_	16.58-6.59
Higher level intra North America
Estimate (Ma)	_	_	_	_	15.75-8.96
95% HPD (Ma)	_	_	_	_	multiple
Higher level intra Asia
Estimate (Ma)	_	_	_	_	9.78-5.28
95% HPD (Ma)	_	_	_	_	multiple
Species stem
Estimate (Ma)	_	_	_	_	11.68-1.3
95% HPD (Ma)	_	_	_	_	multiple
Fossil calibrations (Ma), Priors used
Vitaceae - Leea	_	85 ± 4.0⁹	85 ± 4.0	90.7 ± 1.0¹⁰	90.7 ± 1.0
Vitis -Parthenocissus	_	58.5 ± 5.0¹¹	_	58.5 ± 5.0	58.5 ± 5.0
Old World - New world Parthenocissus	_	_	21.6 ± 6.4¹²	_	_
Within Vitis	_	_	4.5 ¹³	5.75 ± 0.5¹⁴	5.75 ± 0.5

¹For nodes "Higher level intra North America", "Higher level intra Asia, "Species stem" the range contains several clades with different estimates, see Figure 3 and Additional file 4 for details, and the 95% HPD included multiple HDP associated with the several clades, see Figure 3. ²one chloroplast gene, 11 diverse Angiosperms; ³4226 nt (2794 cpDNA + 1432 nDNA); ⁴3583 nt (2701 cpDNA + 882 nDNA); ⁵estimates from analyses that either constrained the stem (first number) or the crown of subgenus Vitis; ⁶5471 nt cpDNA;⁷11,440 nt, 27 nuclear gene fragments; ⁸dash: information is not applicable; ⁹Wikström et al. [56] used a 3-gene data set, rate smoothing, and a single calibration point to estimate the stem age of Vitaceae at 78 - 92 Ma from which the prior distribution was derived; ¹⁰estimate from Magallón and Castillo [57] because Liu et al. [35] agree with arguments made by Nie et al. [58] that the previous Vitaceae stem age estimate [56] was inaccurate; ¹¹stem age of the Vitis-Ampelocissus clade, located in the Paleocene to which the oldest reliable Vitaceae fossils date, including Ampelopsis, Ampelocissus and Vitis[35]; ¹²prior based on estimates by Nie et al. [35]; ¹³minimum age constraint based on fossil seeds described by Gong et al. [59]; ¹⁴based on fossil relatives of V. labrusca described by Gong et al. [59].

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