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Citation for Study 1548

Citation title: "Dating Dispersal and Radiation in the Gymnosperm Gnetum (Gnetales) ?? clock calibration when outgroup relationships are uncertain.".

This study was previously identified under the legacy study ID S1493 (Status: Published).

Citation

Won H., & Renner S.S. 2006. Dating Dispersal and Radiation in the Gymnosperm Gnetum (Gnetales) ?? clock calibration when outgroup relationships are uncertain. Systematic Biology, 55(4): 610-622.

Authors

• Won H.
• Renner S.S. 011-49-(0)89-17861250

Abstract

Most implementations of molecular clocks require resolved topologies. However, one of the Bayesian relaxed clock approaches accepts input topologies that include polytomies. We explored the effects of resolved and unresolved input topologies in a rate-heterogeneous sequence data set for Gnetum, a member of the seed plant lineage Gnetales. Gnetum, which has no fossil record, has ten species in South America, one in tropical West Africa, and 20-25 in tropical Asia, and explanations for the ages of these disjunctions involve long distance dispersal and/or the breakup of Gondwana. The other two genera of Gnetales, as well as conifers, Ginkgo, cycads, and angiosperms, have fossil records that can serve to constrain divergence events in Gnetum and thus obtain absolute time estimates for the geographic disjunctions. To resolve relationships within Gnetum, we sequenced most of its species for six loci from the chloroplast (rbcL, matK, and the trnT-trnF region), the nucleus (rITS/5.8S and the LEAFY gene second intron), and the mitochondrion (nad1 gene second intron). We then applied different clock approaches and outgroup topologies because relationships among the major seed plant lineages are currently unresolved. For a small set of Gnetales exemplars (n =13) in which rbcL and matK satisfied the clock assumption, we obtained time estimates from a strict clock, calibrated with one outgroup fossil. We then re-estimated divergence times based on a larger sample of seed plants (n = 38), using a relaxed Bayesian clock, multiple fossil constraints, and differently resolved topologies, including one that contained a basal polytomy among gymnosperms. The changing hierarchical relationships among seed plants (and accordingly changing placements of distant calibration fossils) resulted in small changes of within-Gnetum estimates because topologically close constraints overrode more distant constraints. Regardless of the seed plant topology assumed, relaxed clock estimates suggest that the extant species groups of Gnetum began diverging from each other during the Upper Oligocene. Strict clock estimates imply a mid-Miocene divergence. These estimates, together with the phylogeny for Gnetum from the six combined data sets, imply that the extant African species of Gnetum is not a remnant of a once Gondwanan distribution. Miocene and Pliocene range expansions are inferred for the Asian subclades of Gnetum, which stem from an ancestor that arrived from Africa. These findings fit with fruit dispersal by water in several species of Gnetum, morphological similarities among apparently young species, and incomplete concerted evolution in the nuclear ITS region.

External links

• DOI: 10.1080/10635150600812619

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1548
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref18190,
  	 author = {Hyosig  Won and Susanne S Renner},
  	 title = {Dating Dispersal and Radiation in the Gymnosperm Gnetum (Gnetales) ?? clock calibration when outgroup relationships are uncertain.},
  	 year = {2006},
  	 keywords = {},
  	 doi = {10.1080/10635150600812619},
  	 url = {},
  	 pmid = {},
  	 journal = {Systematic Biology},
  	 volume = {55},
  	 number = {4},
  	 pages = {610--622},
  	 abstract = {Most implementations of molecular clocks require resolved topologies. However, one of the Bayesian relaxed clock approaches accepts input topologies that include polytomies. We explored the effects of resolved and unresolved input topologies in a rate-heterogeneous sequence data set for Gnetum, a member of the seed plant lineage Gnetales. Gnetum, which has no fossil record, has ten species in South America, one in tropical West Africa, and 20-25 in tropical Asia, and explanations for the ages of these disjunctions involve long distance dispersal and/or the breakup of Gondwana. The other two genera of Gnetales, as well as conifers, Ginkgo, cycads, and angiosperms, have fossil records that can serve to constrain divergence events in Gnetum and thus obtain absolute time estimates for the geographic disjunctions. To resolve relationships within Gnetum, we sequenced most of its species for six loci from the chloroplast (rbcL, matK, and the trnT-trnF region), the nucleus (rITS/5.8S and the LEAFY gene second intron), and the mitochondrion (nad1 gene second intron). We then applied different clock approaches and outgroup topologies because relationships among the major seed plant lineages are currently unresolved. For a small set of Gnetales exemplars (n =13) in which rbcL and matK satisfied the clock assumption, we obtained time estimates from a strict clock, calibrated with one outgroup fossil. We then re-estimated divergence times based on a larger sample of seed plants (n = 38), using a relaxed Bayesian clock, multiple fossil constraints, and differently resolved topologies, including one that contained a basal polytomy among gymnosperms. The changing hierarchical relationships among seed plants (and accordingly changing placements of distant calibration fossils) resulted in small changes of within-Gnetum estimates because topologically close constraints overrode more distant constraints. Regardless of the seed plant topology assumed, relaxed clock estimates suggest that the extant species groups of Gnetum began diverging from each other during the Upper Oligocene. Strict clock estimates imply a mid-Miocene divergence. These estimates, together with the phylogeny for Gnetum from the six combined data sets, imply that the extant African species of Gnetum is not a remnant of a once Gondwanan distribution. Miocene and Pliocene range expansions are inferred for the Asian subclades of Gnetum, which stem from an ancestor that arrived from Africa. These findings fit with fruit dispersal by water in several species of Gnetum, morphological similarities among apparently young species, and incomplete concerted evolution in the nuclear ITS region.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 18190
  AU  - Won,Hyosig 
  AU  - Renner,Susanne S
  T1  - Dating Dispersal and Radiation in the Gymnosperm Gnetum (Gnetales) ?? clock calibration when outgroup relationships are uncertain.
  PY  - 2006
  KW  - 
  UR  - http://dx.doi.org/10.1080/10635150600812619
  N2  - Most implementations of molecular clocks require resolved topologies. However, one of the Bayesian relaxed clock approaches accepts input topologies that include polytomies. We explored the effects of resolved and unresolved input topologies in a rate-heterogeneous sequence data set for Gnetum, a member of the seed plant lineage Gnetales. Gnetum, which has no fossil record, has ten species in South America, one in tropical West Africa, and 20-25 in tropical Asia, and explanations for the ages of these disjunctions involve long distance dispersal and/or the breakup of Gondwana. The other two genera of Gnetales, as well as conifers, Ginkgo, cycads, and angiosperms, have fossil records that can serve to constrain divergence events in Gnetum and thus obtain absolute time estimates for the geographic disjunctions. To resolve relationships within Gnetum, we sequenced most of its species for six loci from the chloroplast (rbcL, matK, and the trnT-trnF region), the nucleus (rITS/5.8S and the LEAFY gene second intron), and the mitochondrion (nad1 gene second intron). We then applied different clock approaches and outgroup topologies because relationships among the major seed plant lineages are currently unresolved. For a small set of Gnetales exemplars (n =13) in which rbcL and matK satisfied the clock assumption, we obtained time estimates from a strict clock, calibrated with one outgroup fossil. We then re-estimated divergence times based on a larger sample of seed plants (n = 38), using a relaxed Bayesian clock, multiple fossil constraints, and differently resolved topologies, including one that contained a basal polytomy among gymnosperms. The changing hierarchical relationships among seed plants (and accordingly changing placements of distant calibration fossils) resulted in small changes of within-Gnetum estimates because topologically close constraints overrode more distant constraints. Regardless of the seed plant topology assumed, relaxed clock estimates suggest that the extant species groups of Gnetum began diverging from each other during the Upper Oligocene. Strict clock estimates imply a mid-Miocene divergence. These estimates, together with the phylogeny for Gnetum from the six combined data sets, imply that the extant African species of Gnetum is not a remnant of a once Gondwanan distribution. Miocene and Pliocene range expansions are inferred for the Asian subclades of Gnetum, which stem from an ancestor that arrived from Africa. These findings fit with fruit dispersal by water in several species of Gnetum, morphological similarities among apparently young species, and incomplete concerted evolution in the nuclear ITS region.
  L3  - 10.1080/10635150600812619
  JF  - Systematic Biology
  VL  - 55
  IS  - 4
  SP  - 610
  EP  - 622
  ER  -