@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. }
}
Matrix 10159 of 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).
Matrices
Title: Single allele matrix
Description: A concatenation of the 18 unlinked loci with selected single alleles. Character (locus) partitions are given in the charset section.
Rows
Taxon Label |
Row Segments |
Characters 1?–30 |
Amytornis ballarae 1a |
(none)
|
CTCCAGCCATGGGACAGAACAAAAGTTGCA |
Amytornis barbatus 3a |
(none)
|
CTCCAGCCACGGGACAGAACAAAAGTTGCA |
Amytornis dorotheae 2a |
(none)
|
CTCCAGCCACGGGACAGAACAAAAGTTGCA |
Amytornis goyderi 1a |
(none)
|
CTCCAGCCGTGGGACAGAACAAAAGTTGCA |
Amytornis housei 1a |
(none)
|
CTCCAGCCACGGGACAGAACAAAAGTTGCA |
Amytornis merrotsyi 1a |
(none)
|
CTCCAGCCACGGGACAGAACATAAGGTGCA |
Amytornis purnelli 1a |
(none)
|
CTCCAGCCATGGGACAGAACAAAAGTTGCA |
Amytornis textilis 1a |
(none)
|
CTCCAGCCACGGGACAGAACAAAAGTTGCA |
Malurus amabilis 1a |
(none)
|
CTCCAGCTACGGGACAGAACAAGAGTTGCA |
Malurus cyaneus 2a |
(none)
|
CTCCAGCTACGGGACAGAACAAAAGTTGCA |
Malurus elegans 1a |
(none)
|
CTCCAGCTACGGGACAGAACAAAAGTTGCA |
Malurus pulcherrimus 1a |
(none)
|
CTCCAGCTACGGGACAGAACAAAAGTTGCA |
Stipiturus malachurus 1a |
(none)
|
CACCAGCCACGGGACAGAACAAAAGTTGCA |
Stipiturus mallee 1a |
(none)
|
CACCAACCACGGGACAGAACAAAAGTTGCA |
Malurus grayi 1a |
(none)
|
CTCCAGCTATGGGGCAGAACAAAAGTTGCA |
Malurus cyanocephalus 1a |
(none)
|
CTCCAGCTACGGGACAGAACAAAAGTTGCA |
Clytomias insignis 1a |
(none)
|
CTCCAGCTATGGGGCAGAACAAAAGTTGCA |
Malurus coronatus 1a |
(none)
|
CTCCAGCTACGGGGCAGAACAAAAGTTGCA |
Malurus melanocephalus 1a |
(none)
|
CTCCAGCTATGGGACAGAACAAAAGTTGCA |
Stipiturus ruficeps 1a |
(none)
|
CACCAACCACGGGACAGAACAAAAGTTGCA |
Malurus splendens 1a |
(none)
|
CTCCAGCTACGGGACAGAACAAAAGTTGCA |
Amytornis striatus 1a |
(none)
|
CTCCAGCCACGGGACAGAACAAAAGTTGCA |
Malurus lamberti 1a |
(none)
|
CTCCAGCTACGGGACAGAACAAAAGTTGCA |
Malurus alboscapulatus 1a |
(none)
|
CTCCAGCTATGGGACAGAACAAAAGTTGCA |
Malurus leucopterus 1a |
(none)
|
CTCCAGCTATGGGACAGAACAAAAGTTGCA |
Gerygone olivacea 1a |
(none)
|
CTCCAGCCATGGGACAGAAAAAAAGTTGCA |
Columns
None of the columns has a description.