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. 2010 Nov;106(5):709-33.
doi: 10.1093/aob/mcq177.

Phylogeny and Biogeography of Allium (Amaryllidaceae: Allieae) Based on Nuclear Ribosomal Internal Transcribed Spacer and Chloroplast rps16 Sequences, Focusing on the Inclusion of Species Endemic to China

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Phylogeny and Biogeography of Allium (Amaryllidaceae: Allieae) Based on Nuclear Ribosomal Internal Transcribed Spacer and Chloroplast rps16 Sequences, Focusing on the Inclusion of Species Endemic to China

Qin-Qin Li et al. Ann Bot. .
Free PMC article

Abstract

Background and aims: The genus Allium comprises more than 800 species, placing it among the largest monocotyledonous genera. It is a variable group that is spread widely across the Holarctic region. Previous studies of Allium have been useful in identifying and assessing its evolutionary lineages. However, there are still many gaps in our knowledge of infrageneric taxonomy and evolution of Allium. Further understanding of its phylogeny and biogeography will be achieved only through continued phylogenetic studies, especially of those species endemic to China that have often been excluded from previous analyses. Earlier molecular studies have shown that Chinese Allium is not monophyletic, so the goal of the present study was to infer the phylogeny and biogeography of Allium and to provide a classification of Chinese Allium by placement of Chinese species in the context of the entire phylogeny.

Methods: Phylogenetic studies were based on sequence data of the nuclear ribosomal internal transcribed spacer (ITS) and chloroplast rps16 intron, analysed using parsimony and Bayesian approaches. Biogeographical patterns were conducted using statistical dispersal-vicariance analysis (S-DIVA).

Key results: Phylogenetic analyses indicate that Allium is monophyletic and consists of three major clades. Optimal reconstructions have favoured the ancestors of Amerallium, Anguinum, Vvedenskya, Porphyroprason and Melanocrommyum as originating in eastern Asia.

Conclusions: Phylogenetic analyses reveal that Allium is monophyletic but that some subgenera are not. The large genetic distances imply that Allium is of ancient origin. Molecular data suggest that its evolution proceeded along three separate evolutionary lines. S-DIVA indicates that the ancestor of Amerallium, Anguinum, Vvedenskya, Porphyroprason and Melanocrommyum originated from eastern Asia and underwent different biogeographical pathways. A taxonomic synopsis of Chinese Allium at sectional level is given, which divides Chinese Allium into 13 subgenera and 34 sections.

Figures

Fig. 1.
Fig. 1.
Phylogenetic tree resulting from a Bayesian analysis of the ITS sequences from species of Allium and ten outgroup species. The subgeneric and sectional classification according to Hanelt et al. (1992), Dubouzet and Shinoda (1999), Friesen et al. (2006), Gurushidze et al. (2008), Nguyen et al. (2008), Kovtonyuk et al. (2009), Fritsch et al. (2010) and our own results is indicated on the right. Values along branches represent Bayesian posterior probabilities (PP) and parsimony bootstrap (BS), respectively. Scientific names given in bold are those endemic to China, in bold italics those distributed in China and other areas, and in italics species distributed in other areas of the world.
Fig. 1.
Fig. 1.
Phylogenetic tree resulting from a Bayesian analysis of the ITS sequences from species of Allium and ten outgroup species. The subgeneric and sectional classification according to Hanelt et al. (1992), Dubouzet and Shinoda (1999), Friesen et al. (2006), Gurushidze et al. (2008), Nguyen et al. (2008), Kovtonyuk et al. (2009), Fritsch et al. (2010) and our own results is indicated on the right. Values along branches represent Bayesian posterior probabilities (PP) and parsimony bootstrap (BS), respectively. Scientific names given in bold are those endemic to China, in bold italics those distributed in China and other areas, and in italics species distributed in other areas of the world.
Fig. 1.
Fig. 1.
Phylogenetic tree resulting from a Bayesian analysis of the ITS sequences from species of Allium and ten outgroup species. The subgeneric and sectional classification according to Hanelt et al. (1992), Dubouzet and Shinoda (1999), Friesen et al. (2006), Gurushidze et al. (2008), Nguyen et al. (2008), Kovtonyuk et al. (2009), Fritsch et al. (2010) and our own results is indicated on the right. Values along branches represent Bayesian posterior probabilities (PP) and parsimony bootstrap (BS), respectively. Scientific names given in bold are those endemic to China, in bold italics those distributed in China and other areas, and in italics species distributed in other areas of the world.
Fig. 1.
Fig. 1.
Phylogenetic tree resulting from a Bayesian analysis of the ITS sequences from species of Allium and ten outgroup species. The subgeneric and sectional classification according to Hanelt et al. (1992), Dubouzet and Shinoda (1999), Friesen et al. (2006), Gurushidze et al. (2008), Nguyen et al. (2008), Kovtonyuk et al. (2009), Fritsch et al. (2010) and our own results is indicated on the right. Values along branches represent Bayesian posterior probabilities (PP) and parsimony bootstrap (BS), respectively. Scientific names given in bold are those endemic to China, in bold italics those distributed in China and other areas, and in italics species distributed in other areas of the world.
Fig. 2.
Fig. 2.
Phylogenetic tree resulting from a Bayesian analysis of combined sequence data (ITS and rps16) focusing on Chinese Allium. The subgeneric and sectional classification according to Hanelt et al. (1992), Dubouzet and Shinoda (1999), Friesen et al. (2006), Nguyen et al. (2008), Kovtonyuk et al. (2009) and our own results is indicated on the right. Values along branches represent Bayesian posterior probabilities (PP) and parsimony bootstrap (BS), respectively. Scientific names given in bold are those endemic to China, in bold italics those distributed in China and other areas, and in italics species distributed in other areas of the world.
Fig. 3.
Fig. 3.
Dispersal–vicariance scenarios for Amerallium and its allies reconstructed by statistical dispersal–vicariance (S-DIVA) optimization with the maximum number of area units set to two. The phylogeny is a Bayesian tree with ambiguities resolved arbitrarily. Pie charts at internal nodes represent the marginal probabilities for each alternative ancestral area derived by using S-DIVA. Triangle: vicariance event; rhomb: duplication event (speciation within the area); arrow (+): dispersal event. Letters denote area units as described in the text.
Fig. 4.
Fig. 4.
Dispersal–vicariance scenarios for Anguinum, Vvedenskya, Porphyroprason, Melanocrommyum and their allies reconstructed by statistical dispersal–vicariance (S-DIVA) optimization with the maximum number of area units set to two. The phylogeny is a Bayesian tree with ambiguities resolved arbitrarily. Pie charts at internal nodes represent the marginal probabilities for each alternative ancestral area derived by using S-DIVA. Triangle: vicariance event; rhomb: duplication event (speciation within the area); arrow (+): dispersal event. Letters denote area units as described in the text.

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