Caryophyllales： Evaluating phylogenetic signal in trnK intron versus matK  

作　　者：Sunny S. CRAWLEY Khidir W. HILU 

机构地区：[1]Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA

出　　处：《Journal of Systematics and Evolution》2012年第5期387-410,共24页植物分类学报（英文版）

基　　金：Acknowledgements We would like to thank Douglas SOLTIS, Pamela SOLTIS, Samuel BROCKINGTON, and Michael MOORE, as well as the Missouri Botanical Garden and the Royal Botanic Garden at Kew for their generosity in providing DNA samples for several taxa. We thank Michelle BARTHET for help in designing one of the primers used here, Anya HINCKLE for helping with specimen collection, Shelli NEWMAN for assistance in lab work, and Gordon BURLEIGH for advice on the data analyses. This work was supported by a grant from the National Science Foundation, USA-EF- 043105 to KWH.

摘　　要：We assess the phylogenetic information in trnK intron at the ordinal level using the Caryophyllales and compare it with that derived from matK. The trnK gene is split into two exons by an intron that includes the matK gene. The plastid trnK is a tRNA gene encoding Lysine（UUU）, whereas the matK gene is a putative group II intron maturase. The two regions are usually coamplified, and trnK intron is partially sequenced but its sequences are often excluded from phylogenetic reconstruction at deep historic levels. This study shows that the two regions are comparable in proportion of variable sites, possess a comparable pattern of substitution rates per site, and display similar phylogenetic informativeness profiles and per-site informativeness. Phylogenetic analyses show strong congruence between phylogenetic trees based on mark and trnK intron partitioned datasets from 45 genera representing 30 of the 34 recognized Caryophyllales families. The trnK intron alone provides a relatively well-resolved topology for the order. Combining the trnK intron with matK sequence data resulted in six most parsimonious trees, differing only in the placement of Claytonia （Portulacaceae） within the noncore group. A well-supported major basal split in the order into core and noncore Caryophyllales with Rhabdodendraceae, Simmondsiaceae, and Asteropeiaceae as sister to remaining core lineages is evident in partitioned and combined analyses. The placement of these three families has been disputable, impacting the overall backbone topology of the Caryophyllales. This study demonstrates the cost effectiveness of using the trnK intron along with matK （both substitutions and insertions/deletions） at deeper phylogenetic level.We assess the phylogenetic information in trnK intron at the ordinal level using the Caryophyllales and compare it with that derived from matK. The trnK gene is split into two exons by an intron that includes the matK gene. The plastid trnK is a tRNA gene encoding Lysine（UUU）, whereas the matK gene is a putative group II intron maturase. The two regions are usually coamplified, and trnK intron is partially sequenced but its sequences are often excluded from phylogenetic reconstruction at deep historic levels. This study shows that the two regions are comparable in proportion of variable sites, possess a comparable pattern of substitution rates per site, and display similar phylogenetic informativeness profiles and per-site informativeness. Phylogenetic analyses show strong congruence between phylogenetic trees based on mark and trnK intron partitioned datasets from 45 genera representing 30 of the 34 recognized Caryophyllales families. The trnK intron alone provides a relatively well-resolved topology for the order. Combining the trnK intron with matK sequence data resulted in six most parsimonious trees, differing only in the placement of Claytonia （Portulacaceae） within the noncore group. A well-supported major basal split in the order into core and noncore Caryophyllales with Rhabdodendraceae, Simmondsiaceae, and Asteropeiaceae as sister to remaining core lineages is evident in partitioned and combined analyses. The placement of these three families has been disputable, impacting the overall backbone topology of the Caryophyllales. This study demonstrates the cost effectiveness of using the trnK intron along with matK （both substitutions and insertions/deletions） at deeper phylogenetic level.

关 键 词：CARYOPHYLLALES MATK phylogenetic informativeness PHYLOGENY trnK intron. 

分 类 号：Q75[生物学—分子生物学] S852.659.5[农业科学—基础兽医学]