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Comparative chloroplast genomics reveals the evolution of Pinaceae genera and subfamilies.

Lin CP, Huang JP, Wu CS, Hsu CY, Chaw SM - Genome Biol Evol (2010)

Bottom Line: We found 21- and 42-kb inversions in congeneric species and different populations of Pinaceous species, which indicates that structural polymorphics may be common and ancient in Pinaceae.Using different maximum-likelihood divergences as thresholds, we conclude that 2 (Abietoideae and Larix-Pseudotsuga-Piceae-Cathaya-Pinus), 4 (Cedrus, non-Cedrus Abietoideae, Larix-Pseudotsuga, and Piceae-Cathaya-Pinus), or 5 (Cedrus, non-Cedrus Abietoideae, Larix-Pseudotsuga, Picea, and Cathaya-Pinus) groups/subfamilies are more reasonable delimitations for Pinaceae.Specifically, our views on subfamilial classifications differ from previous studies in terms of the rank of Cedrus and with recognition of more than two subfamilies.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan.

ABSTRACT
As the largest and the basal-most family of conifers, Pinaceae provides key insights into the evolutionary history of conifers. We present comparative chloroplast genomics and analysis of concatenated 49 chloroplast protein-coding genes common to 19 gymnosperms, including 15 species from 8 Pinaceous genera, to address the long-standing controversy about Pinaceae phylogeny. The complete cpDNAs of Cathaya argyrophylla and Cedrus deodara (Abitoideae) and draft cpDNAs of Larix decidua, Picea morrisonicola, and Pseudotsuga wilsoniana are reported. We found 21- and 42-kb inversions in congeneric species and different populations of Pinaceous species, which indicates that structural polymorphics may be common and ancient in Pinaceae. Our phylogenetic analyses reveal that Cedrus is clustered with Abies-Keteleeria rather than the basal-most genus of Pinaceae and that Cathaya is closer to Pinus than to Picea or Larix-Pseudotsuga. Topology and structural change tests and indel-distribution comparisons lend further evidence to our phylogenetic finding. Our molecular datings suggest that Pinaceae first evolved during Early Jurassic, and diversification of Pinaceous subfamilies and genera took place during Mid-Jurassic and Lower Cretaceous, respectively. Using different maximum-likelihood divergences as thresholds, we conclude that 2 (Abietoideae and Larix-Pseudotsuga-Piceae-Cathaya-Pinus), 4 (Cedrus, non-Cedrus Abietoideae, Larix-Pseudotsuga, and Piceae-Cathaya-Pinus), or 5 (Cedrus, non-Cedrus Abietoideae, Larix-Pseudotsuga, Picea, and Cathaya-Pinus) groups/subfamilies are more reasonable delimitations for Pinaceae. Specifically, our views on subfamilial classifications differ from previous studies in terms of the rank of Cedrus and with recognition of more than two subfamilies.

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Related in: MedlinePlus

Six major competing views on the phylogeny of Pinaceous genera and subfamilies. All trees were redrawn and simplified from the cited references. The light, medium, and heavy gray backgrounds indicate the positions of Cathaya, Pseudotsuga, and Cedrus, respectively. Prior treatments without phylogenetic trees were not included. Modified trees were reconstructed using characters noted within the parentheses below cited studies. For subfamilial delimitations, refer to supplementary table 1 (Supplementary Material online) and text.
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fig1: Six major competing views on the phylogeny of Pinaceous genera and subfamilies. All trees were redrawn and simplified from the cited references. The light, medium, and heavy gray backgrounds indicate the positions of Cathaya, Pseudotsuga, and Cedrus, respectively. Prior treatments without phylogenetic trees were not included. Modified trees were reconstructed using characters noted within the parentheses below cited studies. For subfamilial delimitations, refer to supplementary table 1 (Supplementary Material online) and text.

Mentions: Six major competing views on the classification/phylogeny of Pinaceae genera and subfamilies (fig. 1; supplementary table 1, Supplementary Material online) have been proposed but debated. The major disputes are in the placements of Cathaya, Cedrus, Pseudolarix, and Pseudotsuga and the delimitation of subfamilies. Van Tieghem (1891) first divided Pinaceae genera into two groups (i.e., the Abietoid [=Abitoideae, including Abies, Cedrus, Keteleeria, Pseudolarix, and Tsuga] and Pinioid [Pinioideae, including Larix, Picea, Pinus, and Pseudotsuga] groups) on the basis of the location and number of resin canals. The two groups were adopted by Jeffrey (1905), Doyle (1945), and Price et al. (1987; Cathaya was not included; fig. 1A) from studies of wood anatomy, pollen morphology, and immunology of seed proteins, respectively. In contrast, Pinus was placed in its own subfamily, Pinioideae, by Vierhapper (1910) because of its unusually short shoots (needle fascicles) and distinctive thickened cone scales (see review by Price 1989). Vierhapper (1910), Pilger (1926), and a number of their followers (e.g., Florin 1931, 1963; Melchior and Werdermann 1954; Krüssmann 1985) divided the remaining genera into two subfamilies (supplementary table 1, Supplementary Material online) on the basis of “presence or absence of strongly condensed vegetative short shoots that bear the majority of the foliage leaves” (Price 1989). However, Price (1989) considered it highly artificial to divide the family on the basis of shoot dimorphism alone, with which other morphological traits show little concordance. Frankis (1988) and Farjon (1990) emphasized the importance of reproductive morphologies, such as cones, seeds, pollen types, and chromosome numbers and concurrently recognized four subfamilies in Pinaceae (supplementary table 1, Supplementary Material online) but disagreed with each other in the divergent course of the subfamilies and the evolutionary position of Cathaya (fig. 1). Wang et al. (2000), using three genes (nad5, matK, and 4CL) for phylogenetic analysis, proposed an eccentric view that Cedrus is the basal-most genus of Pinaceae. By inferring from chloroplast rbcL and matK genes and nonmolecular characters and integrating fossil and extant Pinaceous taxa, Gernandt et al. (2008) claimed that root placements varied for Pinaceae when different analysis methods were conducted.


Comparative chloroplast genomics reveals the evolution of Pinaceae genera and subfamilies.

Lin CP, Huang JP, Wu CS, Hsu CY, Chaw SM - Genome Biol Evol (2010)

Six major competing views on the phylogeny of Pinaceous genera and subfamilies. All trees were redrawn and simplified from the cited references. The light, medium, and heavy gray backgrounds indicate the positions of Cathaya, Pseudotsuga, and Cedrus, respectively. Prior treatments without phylogenetic trees were not included. Modified trees were reconstructed using characters noted within the parentheses below cited studies. For subfamilial delimitations, refer to supplementary table 1 (Supplementary Material online) and text.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2997556&req=5

fig1: Six major competing views on the phylogeny of Pinaceous genera and subfamilies. All trees were redrawn and simplified from the cited references. The light, medium, and heavy gray backgrounds indicate the positions of Cathaya, Pseudotsuga, and Cedrus, respectively. Prior treatments without phylogenetic trees were not included. Modified trees were reconstructed using characters noted within the parentheses below cited studies. For subfamilial delimitations, refer to supplementary table 1 (Supplementary Material online) and text.
Mentions: Six major competing views on the classification/phylogeny of Pinaceae genera and subfamilies (fig. 1; supplementary table 1, Supplementary Material online) have been proposed but debated. The major disputes are in the placements of Cathaya, Cedrus, Pseudolarix, and Pseudotsuga and the delimitation of subfamilies. Van Tieghem (1891) first divided Pinaceae genera into two groups (i.e., the Abietoid [=Abitoideae, including Abies, Cedrus, Keteleeria, Pseudolarix, and Tsuga] and Pinioid [Pinioideae, including Larix, Picea, Pinus, and Pseudotsuga] groups) on the basis of the location and number of resin canals. The two groups were adopted by Jeffrey (1905), Doyle (1945), and Price et al. (1987; Cathaya was not included; fig. 1A) from studies of wood anatomy, pollen morphology, and immunology of seed proteins, respectively. In contrast, Pinus was placed in its own subfamily, Pinioideae, by Vierhapper (1910) because of its unusually short shoots (needle fascicles) and distinctive thickened cone scales (see review by Price 1989). Vierhapper (1910), Pilger (1926), and a number of their followers (e.g., Florin 1931, 1963; Melchior and Werdermann 1954; Krüssmann 1985) divided the remaining genera into two subfamilies (supplementary table 1, Supplementary Material online) on the basis of “presence or absence of strongly condensed vegetative short shoots that bear the majority of the foliage leaves” (Price 1989). However, Price (1989) considered it highly artificial to divide the family on the basis of shoot dimorphism alone, with which other morphological traits show little concordance. Frankis (1988) and Farjon (1990) emphasized the importance of reproductive morphologies, such as cones, seeds, pollen types, and chromosome numbers and concurrently recognized four subfamilies in Pinaceae (supplementary table 1, Supplementary Material online) but disagreed with each other in the divergent course of the subfamilies and the evolutionary position of Cathaya (fig. 1). Wang et al. (2000), using three genes (nad5, matK, and 4CL) for phylogenetic analysis, proposed an eccentric view that Cedrus is the basal-most genus of Pinaceae. By inferring from chloroplast rbcL and matK genes and nonmolecular characters and integrating fossil and extant Pinaceous taxa, Gernandt et al. (2008) claimed that root placements varied for Pinaceae when different analysis methods were conducted.

Bottom Line: We found 21- and 42-kb inversions in congeneric species and different populations of Pinaceous species, which indicates that structural polymorphics may be common and ancient in Pinaceae.Using different maximum-likelihood divergences as thresholds, we conclude that 2 (Abietoideae and Larix-Pseudotsuga-Piceae-Cathaya-Pinus), 4 (Cedrus, non-Cedrus Abietoideae, Larix-Pseudotsuga, and Piceae-Cathaya-Pinus), or 5 (Cedrus, non-Cedrus Abietoideae, Larix-Pseudotsuga, Picea, and Cathaya-Pinus) groups/subfamilies are more reasonable delimitations for Pinaceae.Specifically, our views on subfamilial classifications differ from previous studies in terms of the rank of Cedrus and with recognition of more than two subfamilies.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan.

ABSTRACT
As the largest and the basal-most family of conifers, Pinaceae provides key insights into the evolutionary history of conifers. We present comparative chloroplast genomics and analysis of concatenated 49 chloroplast protein-coding genes common to 19 gymnosperms, including 15 species from 8 Pinaceous genera, to address the long-standing controversy about Pinaceae phylogeny. The complete cpDNAs of Cathaya argyrophylla and Cedrus deodara (Abitoideae) and draft cpDNAs of Larix decidua, Picea morrisonicola, and Pseudotsuga wilsoniana are reported. We found 21- and 42-kb inversions in congeneric species and different populations of Pinaceous species, which indicates that structural polymorphics may be common and ancient in Pinaceae. Our phylogenetic analyses reveal that Cedrus is clustered with Abies-Keteleeria rather than the basal-most genus of Pinaceae and that Cathaya is closer to Pinus than to Picea or Larix-Pseudotsuga. Topology and structural change tests and indel-distribution comparisons lend further evidence to our phylogenetic finding. Our molecular datings suggest that Pinaceae first evolved during Early Jurassic, and diversification of Pinaceous subfamilies and genera took place during Mid-Jurassic and Lower Cretaceous, respectively. Using different maximum-likelihood divergences as thresholds, we conclude that 2 (Abietoideae and Larix-Pseudotsuga-Piceae-Cathaya-Pinus), 4 (Cedrus, non-Cedrus Abietoideae, Larix-Pseudotsuga, and Piceae-Cathaya-Pinus), or 5 (Cedrus, non-Cedrus Abietoideae, Larix-Pseudotsuga, Picea, and Cathaya-Pinus) groups/subfamilies are more reasonable delimitations for Pinaceae. Specifically, our views on subfamilial classifications differ from previous studies in terms of the rank of Cedrus and with recognition of more than two subfamilies.

Show MeSH
Related in: MedlinePlus