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

Native geographic distribution of the genus Vitis (grey shading1) and geographic regions of origin of Vitis species used in this study. Dashed lines indicate southern borders of the polar ice cap during the most recent ice age2. Dash-dot lines indicate ice age refugia of the forest flora2. Areas labeled 1 through 4 were used in ancestral area optimization (reversible parsimony, Additional file 14). Redrawn from 1Alleweldt et al. [7], 2Reinig [14].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Native geographic distribution of the genus Vitis (grey shading1) and geographic regions of origin of Vitis species used in this study. Dashed lines indicate southern borders of the polar ice cap during the most recent ice age2. Dash-dot lines indicate ice age refugia of the forest flora2. Areas labeled 1 through 4 were used in ancestral area optimization (reversible parsimony, Additional file 14). Redrawn from 1Alleweldt et al. [7], 2Reinig [14].

Mentions: Centers of grapevine diversity are found in the southeastern US [3-5] and East Asia [4,6]. Up to 30 species are native to a vast area in eastern Asia, China, Japan and Java, two species across middle Asia and Europe, and up to 28 species across the eastern and southwestern US and Mexico [2] (Figure 1). Appendix 1 expands discussion of the biogeographic background. The genus Vitis is divided into two subgenera: Muscadinia Planch. (2n = 40, one or two species) and Vitis Planch. (2n = 38, the remaining species). Additional divisions within Vitis are “series” which are subgeneric groupings that have been used historically in the systematics of Vitis. They rank below “sections” that are more commonly used in plant systematics for groups of species. Although all wild species are considered diploid, there is evidence of hexaploidization in their distant past [7-9] that is shared with all rosids [9]. The two subgenera are nearly reproductively isolated while the species within subgenus Vitis are interfertile. All species are dioecious except V. vinifera which has hermaphroditic flowers, and V. rotundifolia Michx. which segregates for this trait. Many species have overlapping distributions, thus natural hybridization would occur were it not for ecological and phenological barriers [3,10,11]. Not surprisingly, the classification of Vitis is confused in part due to the lack of agreement among systematic botanists as to what constitutes a true species and because of extreme morphological variation within the species [2,3,7]. This has led to many extraneous species names [7,12]. The systematics of Vitis is based primarily on morphology [13] and molecular methods have only recently been used to study this taxonomic problem.


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)

Native geographic distribution of the genus Vitis (grey shading1) and geographic regions of origin of Vitis species used in this study. Dashed lines indicate southern borders of the polar ice cap during the most recent ice age2. Dash-dot lines indicate ice age refugia of the forest flora2. Areas labeled 1 through 4 were used in ancestral area optimization (reversible parsimony, Additional file 14). Redrawn from 1Alleweldt et al. [7], 2Reinig [14].
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Native geographic distribution of the genus Vitis (grey shading1) and geographic regions of origin of Vitis species used in this study. Dashed lines indicate southern borders of the polar ice cap during the most recent ice age2. Dash-dot lines indicate ice age refugia of the forest flora2. Areas labeled 1 through 4 were used in ancestral area optimization (reversible parsimony, Additional file 14). Redrawn from 1Alleweldt et al. [7], 2Reinig [14].
Mentions: Centers of grapevine diversity are found in the southeastern US [3-5] and East Asia [4,6]. Up to 30 species are native to a vast area in eastern Asia, China, Japan and Java, two species across middle Asia and Europe, and up to 28 species across the eastern and southwestern US and Mexico [2] (Figure 1). Appendix 1 expands discussion of the biogeographic background. The genus Vitis is divided into two subgenera: Muscadinia Planch. (2n = 40, one or two species) and Vitis Planch. (2n = 38, the remaining species). Additional divisions within Vitis are “series” which are subgeneric groupings that have been used historically in the systematics of Vitis. They rank below “sections” that are more commonly used in plant systematics for groups of species. Although all wild species are considered diploid, there is evidence of hexaploidization in their distant past [7-9] that is shared with all rosids [9]. The two subgenera are nearly reproductively isolated while the species within subgenus Vitis are interfertile. All species are dioecious except V. vinifera which has hermaphroditic flowers, and V. rotundifolia Michx. which segregates for this trait. Many species have overlapping distributions, thus natural hybridization would occur were it not for ecological and phenological barriers [3,10,11]. Not surprisingly, the classification of Vitis is confused in part due to the lack of agreement among systematic botanists as to what constitutes a true species and because of extreme morphological variation within the species [2,3,7]. This has led to many extraneous species names [7,12]. The systematics of Vitis is based primarily on morphology [13] and molecular methods have only recently been used to study this taxonomic problem.

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