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

Wan Y, Schwaninger HR, Baldo AM, Labate JA, Zhong GY, Simon CJ - BMC Evol. Biol. (2013)

Bottom Line: Several species had species-specific SNPs.NeighborNet analysis showed extensive reticulation at the core of subgenus Vitis representing the deeper nodes, with extensive reticulation radiating outward.Fitch Parsimony identified North America as the origin of the most recent common ancestor of extant Vitis species.

View Article: PubMed Central - HTML - PubMed

Affiliation: College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.

ABSTRACT

Background: Grapes are one of the most economically important fruit crops. There are about 60 species in the genus Vitis. The phylogenetic relationships among these species are of keen interest for the conservation and use of this germplasm. We selected 309 accessions from 48 Vitis species,varieties, and outgroups, examined ~11 kb (~3.4 Mb total) of aligned nuclear DNA sequences from 27 unlinked genes in a phylogenetic context, and estimated divergence times based on fossil calibrations.

Results: Vitis formed a strongly supported clade. There was substantial support for species and less for the higher-level groupings (series). As estimated from extant taxa, the crown age of Vitis was 28 Ma and the divergence of subgenera (Vitis and Muscadinia) occurred at ~18 Ma. Higher clades in subgenus Vitis diverged 16 - 5 Ma with overlapping confidence intervals, and ongoing divergence formed extant species at 12 - 1.3 Ma. Several species had species-specific SNPs. NeighborNet analysis showed extensive reticulation at the core of subgenus Vitis representing the deeper nodes, with extensive reticulation radiating outward. Fitch Parsimony identified North America as the origin of the most recent common ancestor of extant Vitis species.

Conclusions: Phylogenetic patterns suggested origination of the genus in North America, fragmentation of an ancestral range during the Miocene, formation of extant species in the late Miocene-Pleistocene, and differentiation of species in the context of Pliocene-Quaternary tectonic and climatic change. Nuclear SNPs effectively resolved relationships at and below the species level in grapes and rectified several misclassifications of accessions in the repositories. Our results challenge current higher-level classifications, reveal the abundance of genetic diversity in the genus that is potentially available for crop improvement, and provide a valuable resource for species delineation, germplasm conservation and use.

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Related in: MedlinePlus

Chronogram of Bayesian divergence time estimates of Vitis diversification based on 27 concatenated nuclear gene fragments inferred using the BEAST software. Grey bars represent the 95% Highest Posterior Density (HPD) intervals of nodal age in million years. Calibration points are indicated with filled circles. Significant evolutionary events are indicated with black diamonds. Asterisk indicates inclusion of a clonally propagated cultivar that may affect the local divergence estimate. Additional files 4 and 5 show nodal ages and posterior probabilities for all nodes in this tree.
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Figure 3: Chronogram of Bayesian divergence time estimates of Vitis diversification based on 27 concatenated nuclear gene fragments inferred using the BEAST software. Grey bars represent the 95% Highest Posterior Density (HPD) intervals of nodal age in million years. Calibration points are indicated with filled circles. Significant evolutionary events are indicated with black diamonds. Asterisk indicates inclusion of a clonally propagated cultivar that may affect the local divergence estimate. Additional files 4 and 5 show nodal ages and posterior probabilities for all nodes in this tree.

Mentions: With the stem age of Vitaceae constrained at 90.7 ± 1.0 Ma, the stem age of Vitis at 58.5 ± 5 Ma, and the divergence of V. labrusca and its closely related North American relatives at 5.75 ± 0.5 Ma, the crown age of Vitis was estimated at 28.32 Ma (95% Highest Posterior Density (HPD) 41.25, 16.23), the crown age of subg. Vitis at 17.82 Ma (95% HPD 26.71,10.14), and the stem ages of most species fell between 11 and 1.3 Ma. The ten individual runs continued for 61.31 million to 89.21 million steps, and estimated the crown age of subg. Vitis between 17.285 Ma and 18.238 Ma. The Bayesian divergence times in Figure 3 were estimated from three combined, unpartitioned runs using BEAST. The maximum clade credibility tree with mean estimates of divergence time for all nodes (Additional file 4) and associated posterior probabilities (Additional file 5) were also obtained.


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

Wan Y, Schwaninger HR, Baldo AM, Labate JA, Zhong GY, Simon CJ - BMC Evol. Biol. (2013)

Chronogram of Bayesian divergence time estimates of Vitis diversification based on 27 concatenated nuclear gene fragments inferred using the BEAST software. Grey bars represent the 95% Highest Posterior Density (HPD) intervals of nodal age in million years. Calibration points are indicated with filled circles. Significant evolutionary events are indicated with black diamonds. Asterisk indicates inclusion of a clonally propagated cultivar that may affect the local divergence estimate. Additional files 4 and 5 show nodal ages and posterior probabilities for all nodes in this tree.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750556&req=5

Figure 3: Chronogram of Bayesian divergence time estimates of Vitis diversification based on 27 concatenated nuclear gene fragments inferred using the BEAST software. Grey bars represent the 95% Highest Posterior Density (HPD) intervals of nodal age in million years. Calibration points are indicated with filled circles. Significant evolutionary events are indicated with black diamonds. Asterisk indicates inclusion of a clonally propagated cultivar that may affect the local divergence estimate. Additional files 4 and 5 show nodal ages and posterior probabilities for all nodes in this tree.
Mentions: With the stem age of Vitaceae constrained at 90.7 ± 1.0 Ma, the stem age of Vitis at 58.5 ± 5 Ma, and the divergence of V. labrusca and its closely related North American relatives at 5.75 ± 0.5 Ma, the crown age of Vitis was estimated at 28.32 Ma (95% Highest Posterior Density (HPD) 41.25, 16.23), the crown age of subg. Vitis at 17.82 Ma (95% HPD 26.71,10.14), and the stem ages of most species fell between 11 and 1.3 Ma. The ten individual runs continued for 61.31 million to 89.21 million steps, and estimated the crown age of subg. Vitis between 17.285 Ma and 18.238 Ma. The Bayesian divergence times in Figure 3 were estimated from three combined, unpartitioned runs using BEAST. The maximum clade credibility tree with mean estimates of divergence time for all nodes (Additional file 4) and associated posterior probabilities (Additional file 5) were also obtained.

Bottom Line: Several species had species-specific SNPs.NeighborNet analysis showed extensive reticulation at the core of subgenus Vitis representing the deeper nodes, with extensive reticulation radiating outward.Fitch Parsimony identified North America as the origin of the most recent common ancestor of extant Vitis species.

View Article: PubMed Central - HTML - PubMed

Affiliation: College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.

ABSTRACT

Background: Grapes are one of the most economically important fruit crops. There are about 60 species in the genus Vitis. The phylogenetic relationships among these species are of keen interest for the conservation and use of this germplasm. We selected 309 accessions from 48 Vitis species,varieties, and outgroups, examined ~11 kb (~3.4 Mb total) of aligned nuclear DNA sequences from 27 unlinked genes in a phylogenetic context, and estimated divergence times based on fossil calibrations.

Results: Vitis formed a strongly supported clade. There was substantial support for species and less for the higher-level groupings (series). As estimated from extant taxa, the crown age of Vitis was 28 Ma and the divergence of subgenera (Vitis and Muscadinia) occurred at ~18 Ma. Higher clades in subgenus Vitis diverged 16 - 5 Ma with overlapping confidence intervals, and ongoing divergence formed extant species at 12 - 1.3 Ma. Several species had species-specific SNPs. NeighborNet analysis showed extensive reticulation at the core of subgenus Vitis representing the deeper nodes, with extensive reticulation radiating outward. Fitch Parsimony identified North America as the origin of the most recent common ancestor of extant Vitis species.

Conclusions: Phylogenetic patterns suggested origination of the genus in North America, fragmentation of an ancestral range during the Miocene, formation of extant species in the late Miocene-Pleistocene, and differentiation of species in the context of Pliocene-Quaternary tectonic and climatic change. Nuclear SNPs effectively resolved relationships at and below the species level in grapes and rectified several misclassifications of accessions in the repositories. Our results challenge current higher-level classifications, reveal the abundance of genetic diversity in the genus that is potentially available for crop improvement, and provide a valuable resource for species delineation, germplasm conservation and use.

Show MeSH
Related in: MedlinePlus