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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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Simplified version (cartoon) of the MP strict consensus tree. Blue = North and Central American accessions, Green = Asian accessions, Red = European accessions. For comparison, Additional files 6 and 10 represent cartoons of the ML and BA trees, respectively.
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Figure 6: Simplified version (cartoon) of the MP strict consensus tree. Blue = North and Central American accessions, Green = Asian accessions, Red = European accessions. For comparison, Additional files 6 and 10 represent cartoons of the ML and BA trees, respectively.

Mentions: TNT’s driven search function produced most parsimonious (MP) trees of the same length in all four searches. The individual MP trees had a score of 4398, consistency index (CI) of 0.360, and retention index (RI) of 0.790. The strict consensus of all 282 MP trees from all four searches had a score of 4580, CI = 0.346, and RI = 0.776. The strict consensus tree was simplified by collapsing terminal clades (Figure 6) for comparisons. The full tree was annotated with support values on selected nodes of interest (Figures 4 and 5, see figure legend). Node numbers are cross referenced with Additional file 11. All node numbers are shown in Additional file 12. The MP bootstrap tree with supports >50% was illustrated (Additional file 13).


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)

Simplified version (cartoon) of the MP strict consensus tree. Blue = North and Central American accessions, Green = Asian accessions, Red = European accessions. For comparison, Additional files 6 and 10 represent cartoons of the ML and BA trees, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Simplified version (cartoon) of the MP strict consensus tree. Blue = North and Central American accessions, Green = Asian accessions, Red = European accessions. For comparison, Additional files 6 and 10 represent cartoons of the ML and BA trees, respectively.
Mentions: TNT’s driven search function produced most parsimonious (MP) trees of the same length in all four searches. The individual MP trees had a score of 4398, consistency index (CI) of 0.360, and retention index (RI) of 0.790. The strict consensus of all 282 MP trees from all four searches had a score of 4580, CI = 0.346, and RI = 0.776. The strict consensus tree was simplified by collapsing terminal clades (Figure 6) for comparisons. The full tree was annotated with support values on selected nodes of interest (Figures 4 and 5, see figure legend). Node numbers are cross referenced with Additional file 11. All node numbers are shown in Additional file 12. The MP bootstrap tree with supports >50% was illustrated (Additional file 13).

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