Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics

Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight famil...

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Published inThe New phytologist Vol. 214; no. 3; pp. 1355 - 1367
Main Authors Zhang, Shu‐Dong, Jin, Jian‐Jun, Chen, Si‐Yun, Chase, Mark W., Soltis, Douglas E., Li, Hong‐Tao, Yang, Jun‐Bo, Li, De‐Zhu, Yi, Ting‐Shuang
Format Journal Article
LanguageEnglish
Published England New Phytologist Trust 01.05.2017
Wiley Subscription Services, Inc
Subjects
Apomixis
Calibration
Comparative analysis
Comparative studies
Cretaceous
Diversification
Fossils
Frameworks
Genetic Variation
Genomics
geological eons
hybridization
Likelihood Functions
monophyly
Nucleotide sequence
Oligocene
Phylogenetics
phylogenomics
Phylogeny
Plastids
Plastids - genetics
plastome
Plastomes
rapid radiation
Rosaceae
Rosaceae - genetics
Rosales
sequence alignment
systematic error
Time Factors
systematic error
rapid radiation
diversification
plastome
phylogenomics
Rosaceae
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Abstract Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family. Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments. Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution.
AbstractList Summary Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family. Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments. Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution.
Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family. Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments. Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution.
Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family. Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments. Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution.Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family. Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments. Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution.
Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family. Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments. Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution.
Summary Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family. Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments. Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution.
* Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. * With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family. * Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics. Three subfamilies and 16 tribes (as previously delimited) were strongly supported as monophyletic, and their relationships were fully resolved and strongly supported at most nodes. Rosaceae were estimated to have originated during the Late Cretaceous with evidence for rapid diversification events during several geological periods. The major lineages rapidly diversified in warm and wet habits during the Late Cretaceous, and the rapid diversification of genera from the early Oligocene onwards occurred in colder and drier environments. * Plastid phylogenomics offers new and important insights into deep phylogenetic relationships and the diversification history of Rosaceae. The robust phylogenetic backbone and time estimates we provide establish a framework for future comparative studies on rosaceous evolution.
Author Jun-Bo Yang
De-Zhu Li
Shu-Dong Zhang
Si-Yun Chen
Douglas E. Soltis
Jian-Jun Jin
Mark W. Chase
Ting-Shuang Yi
Hong-Tao Li
Author_xml – sequence: 1
  givenname: Shu‐Dong
  surname: Zhang
  fullname: Zhang, Shu‐Dong
  organization: Chinese Academy of Sciences
– sequence: 2
  givenname: Jian‐Jun
  surname: Jin
  fullname: Jin, Jian‐Jun
  organization: University of Chinese Academy of Sciences
– sequence: 3
  givenname: Si‐Yun
  surname: Chen
  fullname: Chen, Si‐Yun
  organization: Chinese Academy of Sciences
– sequence: 4
  givenname: Mark W.
  surname: Chase
  fullname: Chase, Mark W.
  organization: University of Western Australia
– sequence: 5
  givenname: Douglas E.
  surname: Soltis
  fullname: Soltis, Douglas E.
  organization: University of Florida
– sequence: 6
  givenname: Hong‐Tao
  surname: Li
  fullname: Li, Hong‐Tao
  organization: Chinese Academy of Sciences
– sequence: 7
  givenname: Jun‐Bo
  surname: Yang
  fullname: Yang, Jun‐Bo
  organization: Chinese Academy of Sciences
– sequence: 8
  givenname: De‐Zhu
  surname: Li
  fullname: Li, De‐Zhu
  email: DZL@mail.kib.ac.cn
  organization: Chinese Academy of Sciences
– sequence: 9
  givenname: Ting‐Shuang
  surname: Yi
  fullname: Yi, Ting‐Shuang
  email: tingshuangyi@mail.kib.ac.cn
  organization: Chinese Academy of Sciences
BackLink https://www.ncbi.nlm.nih.gov/pubmed/28186635$$D View this record in MEDLINE/PubMed
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Issue 3
Keywords systematic error
rapid radiation
diversification
plastome
phylogenomics
Rosaceae
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Snippet Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their...
Summary Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their...
Summary Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their...
* Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their...
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StartPage 1355
SubjectTerms Apomixis
Calibration
Comparative analysis
Comparative studies
Cretaceous
Diversification
Fossils
Frameworks
Genetic Variation
Genomics
geological eons
hybridization
Likelihood Functions
monophyly
Nucleotide sequence
Oligocene
Phylogenetics
phylogenomics
Phylogeny
Plastids
Plastids - genetics
plastome
Plastomes
rapid radiation
Rosaceae
Rosaceae - genetics
Rosales
sequence alignment
systematic error
Time Factors
Title Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics
URI https://www.jstor.org/stable/90004239
https://onlinelibrary.wiley.com/doi/abs/10.1111%2Fnph.14461
https://www.ncbi.nlm.nih.gov/pubmed/28186635
https://www.proquest.com/docview/1886200210
https://www.proquest.com/docview/2064676988
https://www.proquest.com/docview/1867547078
https://www.proquest.com/docview/1891882617
https://www.proquest.com/docview/2000508607
Volume 214
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