@ARTICLE{TreeBASE2Ref23084,
author = {Sidonie Bellot and Susanne S Renner},
title = {Exploring New Dating Approaches for Parasites: The Worldwide Apodanthaceae (Cucurbitales) as an Example.},
year = {2014},
keywords = {Local clocks, molecular clocks, parasitic plants, random local clocks, substitution rates, uncorrelated lognormal clock, Bayes factors, model selection},
doi = {},
url = {http://},
pmid = {},
journal = {Molecular Phylogenetics and Evolution},
volume = {},
number = {},
pages = {},
abstract = {Gene trees of holoparasitic plants usually show distinctly longer branch lengths than seen in photosynthetic closest relatives. Such substitution rate jumps have made it difficult to infer the absolute divergence times of parasites. An additional problem is that parasite clades often lack a fossil record. Using nuclear and mitochondrial DNA sequences of Apodanthaceae, a worldwide family of endoparasites living inside Fabaceae and Salicaceae, we compared several new dating approaches: (i) an uncorrelated lognormal (UCLN) model calibrated with outgroup fossils, (ii) ages of host lineages as a maximal age in an UCLN model, (iii) user-assigned local clocks (LC), and (iv) outgroup-fossil-calibrated random local clocks (RLC) with varying prior probabilities on the number of rate changes (RLCu model, RLCp model). The resulting dated phylogenies include all 10 species of the family, three in Australia, one in Iran, one in Africa, and the remainder in the Americas. All clock models infer a drastic rate jump between nonparasitic outgroups and Apodanthaceae, but since they distribute the rate heterogeneity differently, they result in much-different age estimates. Because the UCLN model is biased against autocorrelation in small datasets and because Bayes factors favor the RLCu model over the RLCp model, we prefer the former, which places the Apodanthaceae stem age at ca. 77 my ago, the divergence between Apodanthes and Pilostyles at 36 my ago, and the crown age of the Australian clade at 8 my ago. In our study system, host-age calibrations did not yield well-constrained results, but random local clocks provided a valuable alternative to the exclusive reliance on UCLN clocks.}
}
Matrix 21678 of Study 15658
Citation title:
"Exploring New Dating Approaches for Parasites: The Worldwide Apodanthaceae (Cucurbitales) as an Example.".
Study name:
"Exploring New Dating Approaches for Parasites: The Worldwide Apodanthaceae (Cucurbitales) as an Example.".
This study is part of submission 15658
(Status: Published).
Matrices
Title: Apodanthaceae 18S 3 mar 2014 MAFFTsec edited
Rows
Taxon Label |
Row Segments |
Characters 1?–30 |
Alnus sinuata |
(none)
|
?????????????????????????????? |
Anisophyllea fallax |
(none)
|
AAGCCAT-GCATGTGTAAGTATGAACAATT |
Apodanthes caseariae Panama Galdames 7260 |
(none)
|
AAGCCAT-GCATGTGCAAGTATGAACGATT |
Apodanthes tribracteata Bolivia Smith 14057 |
(none)
|
AAGCCAT-GCATGTGCA-GTATGAACGATT |
Betula pendula |
(none)
|
?????????????????????????????? |
Clusia rosea |
(none)
|
???CCAT-GCATGTGTAAGTATGAACTAAT |
Coccinia adoensis |
(none)
|
AAGCCAT-GCATGTGTAAGTATGAACTAAT |
Corynocarpus laevigatus |
(none)
|
AAGCCAT-GCATGTGTAAGTATGAACTAAT |
Cucumis sativus |
(none)
|
AAGCCAT-GCATGTGTAAGTATGAACTAAT |
Cucurbita pepo |
(none)
|
AAGCCAT-GCATGTGTAAGTATGAACTAAT |
Datisca glomerata |
(none)
|
AAGCCAT-GCATGTGTAAGTATGAACTAGT |
Fagus grandifolia |
(none)
|
AAGCCAT-GCATGTGTAAGTATGAACTAAT |
Juglans mandshurica |
(none)
|
?????????????????????????????? |
Nothofagus antarctica |
(none)
|
?????????????????????????????? |
Pilostyles aethiopica Zimbabwe Bellot 29 |
(none)
|
AAGCCAT-GCACGTGCGAGTATGAACGATT |
Pilostyles berteroi Chile Heibl 05017 |
(none)
|
AAGCCAT-GCATGTGCAAGTATGAACGAGT |
Pilostyles calliandrae Brazil Heringer 5768 |
(none)
|
AAGCCAT-GCATGTGCAAGTATGAACGAGT |
Pilostyles coccoidea Australia Thiele 3495 |
(none)
|
AAGCCATCGCATGTGC{CG}AGTATGAACG |
Pilostyles collina Australia Thiele 4501 |
(none)
|
{AC}AGCCAT-GCATGTGCGAGTATGAACG |
Pilostyles goyazensis Brazil Irwin 14880 |
(none)
|
?AGCCAT-GCATGTGCA-GTATGAACGAGT |
Pilostyles hamiltonii Australia Dixon 1039 |
(none)
|
?????????????????????????????? |
Pilostyles haussknechtii Iran Chehregani 17834 |
(none)
|
AAGCCAT-GCATGTGCGAGTATGAACGATT |
Pilostyles ingae Brazil Glaziou 22029 |
(none)
|
????????????GTGCA-GTATGAACGAGT |
Pilostyles mexicana Mexico Breedlove 27233 |
(none)
|
AAGCCAT-GCATGTGCA-GTATGAACGAGT |
Pilostyles mortoni Mexico Wynd 256 |
(none)
|
TAGCCAT-GCATGTGCA-GTATGAACGAGT |
Pilostyles thurberi Mexico Johnston 11286 |
(none)
|
?AGCCAT-GCATGTGCA-GTATGAACGAGT |
Pilostyles ulei Bolivia Nee 48695 |
(none)
|
?????????????????????????????? |
Pilostyles ulei Brazil Ceccantini 3593 |
(none)
|
AAGCCAT-GCATGTGCAAGTATGAACGAGT |
Columns
None of the columns has a description.