Abstract
The number, size, and scope of phylogenetic analyses using molecular data has increased steadily in recent years. This has simultaneously led to a dramatic improvement in our understanding of phylogenetic relationships and a better appreciation for an array of methodological problems that continue to hinder progress in phylogenetic studies of certain data sets and/or particular parts of the tree of life. This review focuses on several persistent problems, including rooting, conflict among data sets, weak support in trees, strong but evidently incorrect support, and the computational issues arising when methods are applied to the large data sets that are becoming increasingly commonplace. We frame each of these issues as a specific problem to be overcome, review the relevant theoretical and empirical literature, and suggest solutions, or at least strategies, for further investigation of the issues involved.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 49-72 |
| Number of pages | 24 |
| Journal | Annual Review of Ecology and Systematics |
| Volume | 33 |
| DOIs | |
| State | Published - 2002 |
| Externally published | Yes |
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Keywords
- Algorithm
- Data partition
- Long-branch attraction
- Model
- Rooting
ASJC Scopus subject areas
- Ecology
Cite this
Troubleshooting molecular phylogenetic analyses. / Sanderson, Michael; Shaffer, H. Bradley.
In: Annual Review of Ecology and Systematics, Vol. 33, 2002, p. 49-72.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Troubleshooting molecular phylogenetic analyses
AU - Sanderson, Michael
AU - Shaffer, H. Bradley
PY - 2002
Y1 - 2002
N2 - The number, size, and scope of phylogenetic analyses using molecular data has increased steadily in recent years. This has simultaneously led to a dramatic improvement in our understanding of phylogenetic relationships and a better appreciation for an array of methodological problems that continue to hinder progress in phylogenetic studies of certain data sets and/or particular parts of the tree of life. This review focuses on several persistent problems, including rooting, conflict among data sets, weak support in trees, strong but evidently incorrect support, and the computational issues arising when methods are applied to the large data sets that are becoming increasingly commonplace. We frame each of these issues as a specific problem to be overcome, review the relevant theoretical and empirical literature, and suggest solutions, or at least strategies, for further investigation of the issues involved.
AB - The number, size, and scope of phylogenetic analyses using molecular data has increased steadily in recent years. This has simultaneously led to a dramatic improvement in our understanding of phylogenetic relationships and a better appreciation for an array of methodological problems that continue to hinder progress in phylogenetic studies of certain data sets and/or particular parts of the tree of life. This review focuses on several persistent problems, including rooting, conflict among data sets, weak support in trees, strong but evidently incorrect support, and the computational issues arising when methods are applied to the large data sets that are becoming increasingly commonplace. We frame each of these issues as a specific problem to be overcome, review the relevant theoretical and empirical literature, and suggest solutions, or at least strategies, for further investigation of the issues involved.
KW - Algorithm
KW - Data partition
KW - Long-branch attraction
KW - Model
KW - Rooting
UR - http://www.scopus.com/inward/record.url?scp=0036926048&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0036926048&partnerID=8YFLogxK
U2 - 10.1146/annurev.ecolsys.33.010802.150509
DO - 10.1146/annurev.ecolsys.33.010802.150509
M3 - Article
AN - SCOPUS:0036926048
VL - 33
SP - 49
EP - 72
JO - Annual Review of Ecology, Evolution, and Systematics
JF - Annual Review of Ecology, Evolution, and Systematics
SN - 1543-592X
ER -