@ARTICLE{TreeBASE2Ref19983,
author = {June Yong Lee and Leo Joseph and Scott V. Edwards},
title = {A Species Tree for the Australo-Papuan Fairy-wrens and Allies (Aves: Maluridae)},
year = {2011},
keywords = {Malurus, Incomplete lineage sorting, indel, Maluridae, species tree, passerine, biogeography},
doi = {},
url = {http://},
pmid = {},
journal = {Systematic Biology},
volume = {},
number = {},
pages = {},
abstract = {We explored the efficacy of species tree methods at the family level in birds, using the Australo-Papuan Fairy-wrens (Passeriformes: Maluridae) as a model system. Fairy-wrens of the genus Malurus are known for high intensities of sexual selection, resulting in some cases in rapid speciation. This history suggests that incomplete lineage sorting (ILS) of neutrally evolving loci could be substantial, a situation that could compromise traditional methods of combining loci in phylogenetic analysis. Using eighteen molecular markers (5 anonymous loci, 7 exons, 5 introns and one mtDNA locus), we show that gene tree monophyly across species could be rejected for 16 out of 18 loci, suggesting substantial ILS at the family level in these birds. Using the software Concaterpillar, we also detect three statistically distinct clusters of gene trees among the 18 loci. Despite substantial variation in gene trees, species trees constructed using four different species tree estimation methods (BEST, BUCKy, and STAR) were generally well-supported and similar to each other and to the concatenation tree, with a few mild discordances at nodes that could explained by rapid and recent speciation events. By contrast, minimizing deep coalescences (MDC) produced a species tree that was topologically more divergent from those of the other methods as measured by multidimensional scaling of trees. Additionally, gene and species trees were topologically more similar in the BEST analysis, presumably because of the species tree prior employed in BEST which appropriately assumes that gene trees are correlated with each other and with the species tree. Among the 18 loci we also discovered 102 independent indel markers, which also proved phylogenetically informative, primarily among genera, and displayed a ~4-fold bias towards deletions. As suggested in earlier work, the grasswrens (Amytornis) are sister to the rest of the family, and the emu-wrens (Stipiturus) are sister to fairy-wrens (Malurus, Clytomias). Our study shows that ILS is common at the family level in birds yet, despite this, species tree methods converge on broadly similar results for this family. }
}
Trees for Study 11849
Citation title:
"A Species Tree for the Australo-Papuan Fairy-wrens and Allies (Aves: Maluridae)".
Study name:
"A Species Tree for the Australo-Papuan Fairy-wrens and Allies (Aves: Maluridae)".
This study is part of submission 11849
(Status: Published).
Trees
ID |
Tree Label |
Tree Title |
Tree Type |
Tree Kind |
Taxa |
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Tr48409
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TNNT3_phyml_genetree |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
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Tr48430
|
Bucky multiple allele |
Australo-Papuan Fairy-wrens |
Single |
Species Tree |
View Taxa
|
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Tr48426
|
phyml |
Australo-Papuan Fairy-wrens |
Single |
Species Tree |
View Taxa
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Tr48420
|
RI2_phyml_genetree |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
|
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|
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Tr48400
|
Full gene tree CDC132 |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
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Tr48407
|
AB4_phyml_genetree |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
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|
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Tr48424
|
mrBayes concatenation |
Australo-Papuan Fairy-wrens |
Single |
Species Tree |
View Taxa
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Tr48432
|
MDC multiple allele |
Australo-Papuan Fairy-wrens |
Single |
Species Tree |
View Taxa
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Tr48404
|
Full gene tree ND2 |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
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Tr48387
|
Full gene tree AL06 |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
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Tr48394
|
Full gene tree PTPN12 |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
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Tr48393
|
Full gene tree MEK1 |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
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Tr48408
|
AL06_phyml_genetree |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
|
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Tr48431
|
MDC single allele |
Australo-Papuan Fairy-wrens |
Single |
Species Tree |
View Taxa
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Tr48391
|
Full gene tree AL28 |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
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|
|
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Tr48416
|
MEK1_phyml_genetree |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
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Tr48396
|
Full gene tree TNNT3 |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
|
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Tr48414
|
HMG_2_phyml_genetree |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
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Tr48405
|
AL28_phyml_genetree |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
|
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Tr48397
|
Full gene tree TRAF6 |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
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Tr48398
|
Full gene tree UBN1 |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
|
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Tr48399
|
Full gene tree AB4 |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
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Tr48427
|
STAR single allele |
Australo-Papuan Fairy-wrens |
Single |
Species Tree |
View Taxa
|
|
|
|
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Tr48412
|
AL26_phyml_genetree |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
|
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Tr48403
|
Full gene tree TGFb2 |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
|
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|
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Tr48410
|
TRAF6_phyml_genetree |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
|
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Tr48419
|
AL16_phyml_genetree |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
|
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|
|
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Tr48390
|
Full gene tree AL26 |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
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Tr48402
|
Full gene tree RI2 |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
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Tr48413
|
PTPN12_phyml_genetree |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
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Tr48395
|
Full gene tree TEX10 |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
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|
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Tr48429
|
Bucky single allele |
Australo-Papuan Fairy-wrens |
Single |
Species Tree |
View Taxa
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Tr48401
|
Full gene tree HMG 2 |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
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Tr48422
|
FSHR_phyml_genetree |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
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Tr48411
|
AL23_phyml_genetree |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
|
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|
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Tr48425
|
PAUP* ML |
Australo-Papuan Fairy-wrens |
Single |
Species Tree |
View Taxa
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Tr48392
|
Full gene tree FSHR |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
|
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|
|
|
Tr48417
|
ND2_phyml_genetree |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
|
|
|
|
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Tr48406
|
CDC132_phyml_genetree |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
|
|
|
|
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Tr48421
|
TGFb2_phyml_genetree |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
|
|
|
|
|
Tr48389
|
Full gene tree AL23 |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
|
|
|
|
|
Tr48423
|
BEST species tree |
Australo-Papuan Fairy-wrens |
Single |
Species Tree |
View Taxa
|
|
|
|
|
Tr48418
|
TEX10_phyml_genetree |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
|
|
|
|
|
Tr48415
|
UBN1_phyml_genetree |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
|
|
|
|
|
Tr48388
|
Full gene tree AL16 |
Australo-Papuan Fairy-wrens |
Single |
Gene Tree |
View Taxa
|
|
|
|
|
Tr48428
|
STAR multiple allele |
Australo-Papuan Fairy-wrens |
Single |
Species Tree |
View Taxa
|
|
|
|
|
Tr48433
|
MDC bootstrap consensus+ |
Australo-Papuan Fairy-wrens |
Single |
Species Tree |
View Taxa
|
|
|
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|