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Cited by 1,162Genomics and Phylogenetic StudiesEvolution and Paleontology StudiesPlant Diversity and Evolution

The DOI matches its Crossref record; 208 of the 208 references it cites were found in a registry or an index.

A review of long-branch attraction

Bergsten, Johannes·2005·Cladistics
DOI 10.1111/j.1096-0031.2005.00059.x
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Abstract

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.

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Research works printed but not linked: 6

  1. Bergsten J., 2004, Acilius phylogeny (Coleoptera: Dytiscidae), problems with long‐branch attraction and morphological intersexual coevlution, Cladistics, 20, 76
  2. Goloboff P., 1999, NONA (NO NAME)
  3. Goloboff P.A., 2004, Cases in which Bayesian phylogenetic analysis will be positively misleading, Cladistics, 20, 83
  4. Huelsenbeck J.P., 1996, Parametric Bootstrapping in Molecular Phylogenetics: Application and Performance
  5. Nixon K., 2002, WinClada
  6. Pickett K.M., 2004, Do Bayesian support values reflect probability of the truth?, Cladistics, 20, 92

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Metadata

Authors
Bergsten, J.
Affiliations
Umeå University (SE)
Corresponding author
Bergsten, Johannes
ORCID
Bergsten, Johannes
Venue
Cladistics
Publisher
Wiley
Published
2005-04
Volume
21
Issue
2
Pages
163-193
ISSN
  • 0748-3007 (ISSN-L)
  • 1096-0031
DOI
10.1111/j.1096-0031.2005.00059.x
OpenAlex
W2101797035
Cited by
1,162
References
203
Citations by year
2026: 32 · 2025: 50 · 2024: 64 · 2023: 54 · 2022: 57 · 2021: 50 · 2020: 71 · 2019: 62 · 2018: 59 · 2017: 72 · 2016: 50 · 2015: 57 · 2014: 69 · 2013: 49 · 2012: 59
FWCI
17.82
Type
journal article
Language
en
Open access
closed
Licence
onlinelibrary.wiley.com/termsAndConditions#vor (vor, 60 d)
Locations
  • Cladistics (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
Keywords
long-branch attraction, outgroup rooting, rasa, split decomposition, spectral analysis, taxon sampling, placental mammals, Cynipidae, murid rodents, tenrecs, guinea pig, Glires, parsimony, Bayesian phylogenetics, codon position

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