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Citation for Study 1208

Citation title: "Multiple calibration points, paleobotanical confidence intervals and the estimation of divergence times: A case study from the birch family (Betulaceae)".

This study was previously identified under the legacy study ID S1121 (Status: Published).

Citation

Forest F., Savolainen V., Chase M., Lupia R., Bruneau A., & Crane P. 2004. Multiple calibration points, paleobotanical confidence intervals and the estimation of divergence times: A case study from the birch family (Betulaceae). Systematic Botany, null.

Authors

• Forest F.
• Savolainen V.
• Chase M.
• Lupia R.
• Bruneau A.
• Crane P.

Abstract

Fossils are widely used as calibration points in molecular-based dating studies and their placement on a phylogenetic tree of extant species is never done without subjectivity. We explore some of the problems linked to calibration with fossils, in particular their position on the tree, and emphasize the use of multiple calibration points to obtain better estimates. We use a phylogenetic analysis of Betulaceae based on nuclear ribosomal DNA sequences (5S spacer and ITS) as a case study and estimated divergence times within the family using the nonparametric rate smoothing method of Sanderson and five calibration points from the extensive fossil record of the family. To assess the effects of assumptions relating to the positions of key fossils with respect to stem lineages versus crown groups, we calculated age estimates by placing each fossil subsequently on the stem lineage node and crown group node, and then determined the median value of the resulting 10 estimates for each node. According to these results, the median values of the crown group and stem lineage of Betulaceae vary from 115.2 to 130.6 million years and 211.2 to 302.6 million years, respectively (branch lengths based on maximum likelihood and DELTRAN and ACCTRAN parsimony estimates). Paleobotanical confidence intervals were determined on the palynological fossil record of Alnus and related extinct genera using methods based on the occurrence of fossils on a stratigraphic column and the lengths of the gaps between these occurrences. The median values of molecular estimates indicate that Betulaceae started to diversify in the Aptian or before, an estimate much older than inferred from the fossil record of triporate pollen. Paleobotanical confidence intervals are more realistic, inferring the earliest appearance of betulaceous components in the Albian-Cenomanian floras. The discrepancy between molecular-based age estimates and the angiosperm fossil record as a whole still needs to be resolved.

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1208
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref15444,
  	 author = {Felix  Forest and Vincent  Savolainen and Mark W.  Chase and Richard  Lupia and Anne  Bruneau and Peter R.  Crane},
  	 title = {Multiple calibration points, paleobotanical confidence intervals and the estimation of divergence times: A case study from the birch family (Betulaceae)},
  	 year = {2004},
  	 keywords = {},
  	 doi = {},
  	 url = {},
  	 pmid = {},
  	 journal = {Systematic Botany},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {Fossils are widely used as calibration points in molecular-based dating studies and their placement on a phylogenetic tree of extant species is never done without subjectivity. We explore some of the problems linked to calibration with fossils, in particular their position on the tree, and emphasize the use of multiple calibration points to obtain better estimates. We use a phylogenetic analysis of Betulaceae based on nuclear ribosomal DNA sequences (5S spacer and ITS) as a case study and estimated divergence times within the family using the nonparametric rate smoothing method of Sanderson and five calibration points from the extensive fossil record of the family. To assess the effects of assumptions relating to the positions of key fossils with respect to stem lineages versus crown groups, we calculated age estimates by placing each fossil subsequently on the stem lineage node and crown group node, and then determined the median value of the resulting 10 estimates for each node. According to these results, the median values of the crown group and stem lineage of Betulaceae vary from 115.2 to 130.6 million years and 211.2 to 302.6 million years, respectively (branch lengths based on maximum likelihood and DELTRAN and ACCTRAN parsimony estimates). Paleobotanical confidence intervals were determined on the palynological fossil record of Alnus and related extinct genera using methods based on the occurrence of fossils on a stratigraphic column and the lengths of the gaps between these occurrences. The median values of molecular estimates indicate that Betulaceae started to diversify in the Aptian or before, an estimate much older than inferred from the fossil record of triporate pollen. Paleobotanical confidence intervals are more realistic, inferring the earliest appearance of betulaceous components in the Albian-Cenomanian floras. The discrepancy between molecular-based age estimates and the angiosperm fossil record as a whole still needs to be resolved.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 15444
  AU  - Forest,Felix 
  AU  - Savolainen,Vincent 
  AU  - Chase,Mark W. 
  AU  - Lupia,Richard 
  AU  - Bruneau,Anne 
  AU  - Crane,Peter R. 
  T1  - Multiple calibration points, paleobotanical confidence intervals and the estimation of divergence times: A case study from the birch family (Betulaceae)
  PY  - 2004
  KW  - 
  UR  - 
  N2  - Fossils are widely used as calibration points in molecular-based dating studies and their placement on a phylogenetic tree of extant species is never done without subjectivity. We explore some of the problems linked to calibration with fossils, in particular their position on the tree, and emphasize the use of multiple calibration points to obtain better estimates. We use a phylogenetic analysis of Betulaceae based on nuclear ribosomal DNA sequences (5S spacer and ITS) as a case study and estimated divergence times within the family using the nonparametric rate smoothing method of Sanderson and five calibration points from the extensive fossil record of the family. To assess the effects of assumptions relating to the positions of key fossils with respect to stem lineages versus crown groups, we calculated age estimates by placing each fossil subsequently on the stem lineage node and crown group node, and then determined the median value of the resulting 10 estimates for each node. According to these results, the median values of the crown group and stem lineage of Betulaceae vary from 115.2 to 130.6 million years and 211.2 to 302.6 million years, respectively (branch lengths based on maximum likelihood and DELTRAN and ACCTRAN parsimony estimates). Paleobotanical confidence intervals were determined on the palynological fossil record of Alnus and related extinct genera using methods based on the occurrence of fossils on a stratigraphic column and the lengths of the gaps between these occurrences. The median values of molecular estimates indicate that Betulaceae started to diversify in the Aptian or before, an estimate much older than inferred from the fossil record of triporate pollen. Paleobotanical confidence intervals are more realistic, inferring the earliest appearance of betulaceous components in the Albian-Cenomanian floras. The discrepancy between molecular-based age estimates and the angiosperm fossil record as a whole still needs to be resolved.
  L3  - 
  JF  - Systematic Botany
  VL  - 
  IS  - 
  ER  -