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A review of long-branch attraction
Umeå University, Faculty of Science and Technology, Ecology and Environmental Science.
2005 (English)In: Cladistics, ISSN 1096-0031, Vol. 21, no 2, 163-193 p.Article in journal (Refereed) Published
Abstract [en]

The history of long-branch attraction, and in particular methods suggested to detect and avoid the artifact to date, is reviewed. Methods suggested to avoid LBA-artifacts include excluding long-branch taxa, excluding faster evolving third codon positions, using inference methods less sensitive to LBA such as likelihood, the Aguinaldo et al. approach, sampling more taxa to break up long branches and sampling more characters especially of another kind, and the pros and cons of these are discussed. Methods suggested to detect LBA are numerous and include methodological disconcordance, RASA, separate partition analyses, parametric simulation, random outgroup sequences, long-branch extraction, split decomposition and spectral analysis. Less than 10 years ago it was doubted if LBA occurred in real datasets. Today, examples are numerous in the literature and it is argued that the development of methods to deal with the problem is warranted. A 16 kbp dataset of placental mammals and a morphological and molecular combined dataset of gall waSPS are used to illustrate the particularly common problem of LBA of problematic ingroup taxa to outgroups. The preferred methods of separate partition analysis, methodological disconcordance, and long branch extraction are used to demonstrate detection methods. It is argued that since outgroup taxa almost always represent long branches and are as such a hazard towards misplacing long branched ingroup taxa, phylogenetic analyses should always be run with and without the outgroups included. This will detect whether only the outgroup roots the ingroup or if it simultaneously alters the ingroup topology, in which case previous studies have shown that the latter is most often the worse. Apart from that LBA to outgroups is the major and most common problem; scanning the literature also detected the ill advised comfort of high support values from thousands of characters, but very few taxa, in the age of genomics. Taxon sampling is crucial for an accurate phylogenetic estimate and trust cannot be put on whole mitochondrial or chloroplast genome studies with only a few taxa, despite their high support values. The placental mammal example demonstrates that parsimony analysis will be prone to LBA by the attraction of the tenrec to the distant marsupial outgroups. In addition, the murid rodents, creating the classic “the guinea-pig is not a rodent” hypothesis in 1996, are also shown to be attracted to the outgroup by nuclear genes, although including the morphological evidence for rodents and Glires overcomes the artifact. The gall wasp example illustrates that Bayesian analyses with a partition-specific GTR + Γ + I model give a conflicting resolution of clades, with a posterior probability of 1.0 when comparing ingroup alone versus outgroup rooted topologies, and this is due to long-branch attraction to the outgroup.


Place, publisher, year, edition, pages
2005. Vol. 21, no 2, 163-193 p.
URN: urn:nbn:se:umu:diva-4560DOI: 10.1111/j.1096-0031.2005.00059.xOAI: diva2:143710
Available from: 2005-05-03 Created: 2005-05-03 Last updated: 2011-03-01Bibliographically approved
In thesis
1. Taxonomy, phylogeny, and secondary sexual character evolution of diving beetles, focusing on the genus Acilius
Open this publication in new window or tab >>Taxonomy, phylogeny, and secondary sexual character evolution of diving beetles, focusing on the genus Acilius
2005 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Sexual conflict can lead to antagonistic coevolution between the sexes, but empirical examples are few. In this thesis secondary sexual characters in diving beetles are interpreted in the light of sexual conflict theory. Whether the male tarsal suction cups and female dorsal modifications are involved in a coevolutionary arms race is tested in two ways. First eight populations of a species with dimorphic females that varied in frequency of the morphs were investigated and male tarsal characteristics quantified. The frequency of female morphs is shown to be significantly correlated to the average number and size of male tarsal suction cups in the population, a prediction of the arms race hypothesis. Second, the hypothesis is tested in a phylogenetic perspective by optimizing the secondary sexual characters on a phylogeny. A full taxonomic revision of the genus Acilius is presented, including new synonyms, lectotype designations, geographic distributions based on more than five thousand examined museum specimens and the description of a new species from northeastern USA. Specimens of all species (except one possibly extinct that failed to be found in Yunnan, China 2000), were field collected between 2000 and 2003 in Sardinia, Sweden, Russia, Honshu and Hokkaido in Japan, New York, Maryland, California and Alberta. Three genes (CO1, H3 and Wingless) were sequenced from the fresh material as well as scoring a morphological character matrix all of which was used to derive a robust and complete hypothesis of the phylogenetic relationship in the group. The phylogeny was derived using Bayesian phylogenetics with Markov Chain Monte Carlo techniques and received a posterior probability of 0.85. Changes in male and female characters turned out to be perfectly correlated across the phylogeny, providing one of the best empirical examples to date of an antagonistic arms race between the sexes in a group of organisms. Finally, a review of a pitfall to phylogenetic analysis known under the name long-branch attraction (LBA), is provided. The problem is well known theoretically but has been questioned to occur in real data, and LBA has been in the core center of the hard debate between parsimony and likelihood advocates since different inference methods vary in sensitivity to the phenomenon. Most important conclusions from the review are; LBA is very common in real data, and is most often introduced with the inclusion of outgroups that almost always provide long branches, pulling down long terminal ingroup branches towards the root. Therefore it is recommended to always run analyses with and without outgroups. Taxon sampling is very important to avoid the pitfall as well as including different kind of data, especially morphological data, i.e. many LBA-affected conclusions have recently been reached by analyses of few taxa with complete genomes. Long-branch extraction (incl. outgroup exclusion), methodological disconcordance (parsimony vs modelbased), separate partition analyses (morphology vs molecules, codon positions, genes, etc), parametric simulation (incl. random outgroups), and split graphs are available relevant methods for the detection of LBA that should be used in combinations, because none alone is enough to stipulate LBA.

Place, publisher, year, edition, pages
Umeå: Ekologi, miljö och geovetenskap, 2005. 36 p.
Biology, antagonistic coevolution, arms race, sexual conflict, diving beetle, Dytiscidae, Coleoptera, taxon sampling, long-branch attraction, parsimony, Bayesian analysis, taxonomic revision, Biologi
National Category
Biological Sciences
urn:nbn:se:umu:diva-527 (URN)91-7305-845-9 (ISBN)
Public defence
2005-06-03, KB3B1, KBC-huset, Umeå Universitet, Umeå, 10:00
Available from: 2005-05-03 Created: 2005-05-03Bibliographically approved

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