Limits...
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.

Show MeSH

Related in: MedlinePlus

Hypothesis of phylogenetic relationships among Vitis species. North America. Strict consensus of 282 most parsimonious trees from four driven searches with support values for selected nodes. Above branches: (Maximum Likelihood BS/ Bayesian PP/ Maximum Parsimony BS). Values can range from 1-100 in ML, 0-1 in BA, 50-100 in MP. Below branches: (node number: branch length/No unique characters/No genes in support of node). The annotation “319: 8/2/6” means that node number 319 has 8 character changes of which 2 are unique to that node, and 6 genes contributed changes. “na” indicates absence of a value in the specific support category. Branch lengths, bootstrap supports, and posterior probabilities for all available branches are shown in Additional files 7, 8, 13, 16. Nodes labeled A-Y are discussed in the text. Figure 4 continues in Figure 5.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3750556&req=5

Figure 4: Hypothesis of phylogenetic relationships among Vitis species. North America. Strict consensus of 282 most parsimonious trees from four driven searches with support values for selected nodes. Above branches: (Maximum Likelihood BS/ Bayesian PP/ Maximum Parsimony BS). Values can range from 1-100 in ML, 0-1 in BA, 50-100 in MP. Below branches: (node number: branch length/No unique characters/No genes in support of node). The annotation “319: 8/2/6” means that node number 319 has 8 character changes of which 2 are unique to that node, and 6 genes contributed changes. “na” indicates absence of a value in the specific support category. Branch lengths, bootstrap supports, and posterior probabilities for all available branches are shown in Additional files 7, 8, 13, 16. Nodes labeled A-Y are discussed in the text. Figure 4 continues in Figure 5.

Mentions: The 20 identical (except for the starting seed) partitioned rapid ML runs using the 273-OTU matrix produced a range of maximum likelihood values of -42511to -42380. The final search on the same matrix following the bootstrap search yielded the highest likelihood value: -42358. This tree was used in comparisons with results from other methods using a cartoon, i.e., a simplified version with collapsed terminal clades (Additional file 6). Bootstrap values are reported for selected nodes (Figures 4 and 5) and all nodes (Additional file 7).


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)

Hypothesis of phylogenetic relationships among Vitis species. North America. Strict consensus of 282 most parsimonious trees from four driven searches with support values for selected nodes. Above branches: (Maximum Likelihood BS/ Bayesian PP/ Maximum Parsimony BS). Values can range from 1-100 in ML, 0-1 in BA, 50-100 in MP. Below branches: (node number: branch length/No unique characters/No genes in support of node). The annotation “319: 8/2/6” means that node number 319 has 8 character changes of which 2 are unique to that node, and 6 genes contributed changes. “na” indicates absence of a value in the specific support category. Branch lengths, bootstrap supports, and posterior probabilities for all available branches are shown in Additional files 7, 8, 13, 16. Nodes labeled A-Y are discussed in the text. Figure 4 continues in Figure 5.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Hypothesis of phylogenetic relationships among Vitis species. North America. Strict consensus of 282 most parsimonious trees from four driven searches with support values for selected nodes. Above branches: (Maximum Likelihood BS/ Bayesian PP/ Maximum Parsimony BS). Values can range from 1-100 in ML, 0-1 in BA, 50-100 in MP. Below branches: (node number: branch length/No unique characters/No genes in support of node). The annotation “319: 8/2/6” means that node number 319 has 8 character changes of which 2 are unique to that node, and 6 genes contributed changes. “na” indicates absence of a value in the specific support category. Branch lengths, bootstrap supports, and posterior probabilities for all available branches are shown in Additional files 7, 8, 13, 16. Nodes labeled A-Y are discussed in the text. Figure 4 continues in Figure 5.
Mentions: The 20 identical (except for the starting seed) partitioned rapid ML runs using the 273-OTU matrix produced a range of maximum likelihood values of -42511to -42380. The final search on the same matrix following the bootstrap search yielded the highest likelihood value: -42358. This tree was used in comparisons with results from other methods using a cartoon, i.e., a simplified version with collapsed terminal clades (Additional file 6). Bootstrap values are reported for selected nodes (Figures 4 and 5) and all nodes (Additional file 7).

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