CoChat
Sign Up
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
Open this paper in CoChat — free account

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.

Overview

Integrity signals

Registry

Crossref · 10.1111/j.1096-0031.2005.00059.x

Cites

208 of 208 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Verification

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Citations

Cites

Show all 203 references

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

Cited by

Sorted by citations

Items 401–500 of 1,000

Related

See all

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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review