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Citation for Study 1658

Citation title: "Evolution of Piperales ?? matK gene and trnK intron sequence data reveal lineage specific resolution contrast".

This study was previously identified under the legacy study ID S1608 (Status: Published).

Citation

Wanke S., Jaramillo M., Borsch T., Samain M., Quandt D., & Neinhuis C. 2006. Evolution of Piperales ?? matK gene and trnK intron sequence data reveal lineage specific resolution contrast. Molecular Phylogenetics and Evolution, null.

Authors

• Wanke S.
• Jaramillo M.
• Borsch T.
• Samain M.
• Quandt D.
• Neinhuis C.

Abstract

Piperales represent the largest basal angiosperm order with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 2000 species), Peperomia (ca. 15001700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (except Hydnoraceae) and all generic segregates (except Euglypha within Aristolochiaceae) of Piperales. A large number of highly informative indels are found in the Piperales trnK/matK dataset. Within a narrow region approximately 500 nt downstream in the matK coding region (CDS), a length variable simple sequence repeat (SSR) expansion segment occurs, in which insertions and deletions have led to short frame-shifts. These are corrected shortly afterwards, resulting in a maximum of six amino acids being affected. Furthermore, additional non-functional matK copies were found in Zippelia begoniifolia, which can easily be discriminated from the functional open reading frame (ORF). The trnK/matK sequence data fully resolve relationships within Peperomia, whereas they are not effective within Piper. The resolution contrast is correlated with the rate heterogeneity between those lineages. Parsimony, Bayesian and likelihood analyses result in virtually the same topology, and converge on the monophyly of Piperaceae and Saururaceae. Lactoris gains high support as sister to Aristolochiaceae subf. Aristolochioideae, but the different tree inference methods yield conflicting results with respect to the relationships of subfam. Asaroideae. In Piperaceae, a clade formed by the monotypic genus Zippelia and the small genus Manekia (=Sarcorhachis) is sister to the two large genera Piper and Peperomia.

External links

• DOI: 10.1016/j.ympev.2006.07.007

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1658
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref18040,
  	 author = {Stefan  Wanke and M. Alejandra  Jaramillo and Thomas  Borsch and M. S.  Samain and Dietmar  Quandt and Cristoph  Neinhuis},
  	 title = {Evolution of Piperales ?? matK gene and trnK intron sequence data reveal lineage specific resolution contrast},
  	 year = {2006},
  	 keywords = {},
  	 doi = {10.1016/j.ympev.2006.07.007},
  	 url = {},
  	 pmid = {},
  	 journal = {Molecular Phylogenetics and Evolution},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {Piperales represent the largest basal angiosperm order with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 2000 species), Peperomia (ca. 15001700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (except Hydnoraceae) and all generic segregates (except Euglypha within Aristolochiaceae) of Piperales. A large number of highly informative indels are found in the Piperales trnK/matK dataset. Within a narrow region approximately 500 nt downstream in the matK coding region (CDS), a length variable simple sequence repeat (SSR) expansion segment occurs, in which insertions and deletions have led to short frame-shifts. These are corrected shortly afterwards, resulting in a maximum of six amino acids being affected. Furthermore, additional non-functional matK copies were found in Zippelia begoniifolia, which can easily be discriminated from the functional open reading frame (ORF). The trnK/matK sequence data fully resolve relationships within Peperomia, whereas they are not effective within Piper. The resolution contrast is correlated with the rate heterogeneity between those lineages. Parsimony, Bayesian and likelihood analyses result in virtually the same topology, and converge on the monophyly of Piperaceae and Saururaceae. Lactoris gains high support as sister to Aristolochiaceae subf. Aristolochioideae, but the different tree inference methods yield conflicting results with respect to the relationships of subfam. Asaroideae. In Piperaceae, a clade formed by the monotypic genus Zippelia and the small genus Manekia (=Sarcorhachis) is sister to the two large genera Piper and Peperomia.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 18040
  AU  - Wanke,Stefan 
  AU  - Jaramillo,M. Alejandra 
  AU  - Borsch,Thomas 
  AU  - Samain,M. S. 
  AU  - Quandt,Dietmar 
  AU  - Neinhuis,Cristoph 
  T1  - Evolution of Piperales ?? matK gene and trnK intron sequence data reveal lineage specific resolution contrast
  PY  - 2006
  KW  - 
  UR  - http://dx.doi.org/10.1016/j.ympev.2006.07.007
  N2  - Piperales represent the largest basal angiosperm order with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 2000 species), Peperomia (ca. 15001700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (except Hydnoraceae) and all generic segregates (except Euglypha within Aristolochiaceae) of Piperales. A large number of highly informative indels are found in the Piperales trnK/matK dataset. Within a narrow region approximately 500 nt downstream in the matK coding region (CDS), a length variable simple sequence repeat (SSR) expansion segment occurs, in which insertions and deletions have led to short frame-shifts. These are corrected shortly afterwards, resulting in a maximum of six amino acids being affected. Furthermore, additional non-functional matK copies were found in Zippelia begoniifolia, which can easily be discriminated from the functional open reading frame (ORF). The trnK/matK sequence data fully resolve relationships within Peperomia, whereas they are not effective within Piper. The resolution contrast is correlated with the rate heterogeneity between those lineages. Parsimony, Bayesian and likelihood analyses result in virtually the same topology, and converge on the monophyly of Piperaceae and Saururaceae. Lactoris gains high support as sister to Aristolochiaceae subf. Aristolochioideae, but the different tree inference methods yield conflicting results with respect to the relationships of subfam. Asaroideae. In Piperaceae, a clade formed by the monotypic genus Zippelia and the small genus Manekia (=Sarcorhachis) is sister to the two large genera Piper and Peperomia.
  L3  - 10.1016/j.ympev.2006.07.007
  JF  - Molecular Phylogenetics and Evolution
  VL  - 
  IS  - 
  ER  -