Extended implied weighting
Open accessAbstract
Several extensions to implied weighting, recently implemented in TNT, allow a better treatment of data sets combining morphological and molecular data sets, as well as those comprising large numbers of missing entries (e.g. palaeontological matrices, or combined matrices with some genes sequenced for few taxa). As there have been recent suggestions that molecular matrices may be better analysed using equal weights (rather than implied weighting), a simple way to apply implied weighting to only some characters (e.g. morphology), leaving other characters with a constant weight (e.g. molecules), is proposed. The new methods also allow weighting entire partitions according to their average homoplasy, giving each of the characters in the partition the same weight (this can be used for dynamically weighting, e.g. entire genes, or first, second, and third positions collectively). Such an approach is easily implemented in schemes like successive weighting, but in the case of implied weighting poses some particular problems. The approach has the peculiar implication that the inclusion of uninformative characters influences the results (by influencing the implied weights for the partitions). Last, the concern that characters with many missing entries may receive artificially inflated weights (because they necessarily display less homoplasy) can be solved by allowing the use of different weighting functions for different characters, in such a way that the cost of additional transformations decreases more rapidly for characters with more missing entries (thus effectively assuming that the unobserved entries are likely to also display some unobserved homoplasy). The conceptual and practical aspects of all these problems, as well as details of the implementation in TNT, are discussed.
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All analyses included implied weighting (XIW) with modifications that prevent improper inflation of weights due to missing entries.
“All of our analyses included implied weighting (XIW) [103], with modifications proposed by [104] that prevent improper inflation of weights due to missing entries (downweighting the weight of characters with missing entries faster).”
From Potential for Powered Flight Neared by Most Close Avialan Relatives, but Few Crossed Its Thresholds (2020) · cites this paper as [104]
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582 · see citing works
TNT, a free program for phylogenetic analysis
Goloboff, P. A., Farris, J. S., & Nixon, K. C. (2008) · Cladistics · doi:10.1111/j.1096-0031.2008.00217.x · Cited by 5,352 · see citing works
Self-citationPARSIMONY JACKKNIFING OUTPERFORMS NEIGHBOR‐JOINING
Farris, J. S., Albert, V. A., Källersjö, M., Lipscomb, D., & Kluge, A. G. (1996) · Cladistics · doi:10.1111/j.1096-0031.1996.tb00196.x · Cited by 1,512 · see citing works
Anisimova, M. O., Gil, M., Dufayard, J.-F., Dessimoz, C., & Gascuel, O. (2011) · Systematic Biology · doi:10.1093/sysbio/syr041 · Cited by 1,299 · see citing works
Estimating character weights during tree search
Goloboff, P. A. (1993) · Cladistics · doi:10.1111/j.1096-0031.1993.tb00209.x · Cited by 1,296 · see citing works
Self-citationA Successive Approximations Approach to Character Weighting
Farris, J. S. (1969) · Systematic Zoology · doi:10.2307/2412182 · Cited by 1,286 · see citing works
Analyzing large data sets in reasonable times: solutions for composite optima
Goloboff, P. A. (1999) · Cladistics · doi:10.1111/j.1096-0031.1999.tb00278.x · Cited by 1,039 · see citing works
Self-citationImprovements to resampling measures of group support
Goloboff, P. A., Farris, J. S., Källersjö, M., Oxelman, B., Ramıacute;rez, M. J., & Szumik, C. A. (2003) · Cladistics · doi:10.1111/j.1096-0031.2003.tb00376.x · Cited by 851 · see citing works
Self-citationWeighting against homoplasy improves phylogenetic analysis of morphological data sets
Goloboff, P. A., Carpenter, J. M., Arias, J. S., & Miranda‐Esquivel, D. R. (2008) · Cladistics · doi:10.1111/j.1096-0031.2008.00209.x · Cited by 566 · see citing works
Self-citationParsimony, Phylogeny, and Genomics
Albert, V. A. (2006) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199297306.001.0001 · Cited by 357 · see citing works
Weighted parsimony phylogeny of the family Characidae (Teleostei: Characiformes)
Mirande, J. M. (2009) · Cladistics · doi:10.1111/j.1096-0031.2009.00262.x · Cited by 323 · see citing works
Homoplasy Increases Phylogenetic Structure
Kälersjö, M., Albert, V. A., & Farris, J. S. (1999) · Cladistics · doi:10.1111/j.1096-0031.1999.tb00400.x · Cited by 297 · see citing works
HomoplasyIncreasesPhylogenetic Structure*1
Kälersjö, M. (1999) · Cladistics · doi:10.1006/clad.1999.0085 · Cited by 230 · see citing works
Dynamic homology and phylogenetic systematics: a unified approach using POY
Wheeler, W. C., Aagesen, L., Arango, C. P., Faivovich, J., Grant, T., D’Haese, C. A., Janies, D. A., Smith, W., Varón, A., & Giribet, G. (2006) · KU ScholarWorks (The University of Kansas) · Cited by 158 · see citing works
Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups
Goloboff, P. A., Catalano, S. A., Mirande, J. M., Szumik, C., Arias, J. S., Källersjö, M., & Farris, J. S. (2009) · Cladistics · doi:10.1111/j.1096-0031.2009.00255.x · Cited by 136 · see citing works
Self-citationGoloboff, P. A. (1997) · Cladistics · doi:10.1111/j.1096-0031.1997.tb00317.x · Cited by 107 · see citing works
Self-citationMETHODS FOR FASTER PARSIMONY ANALYSIS
Goloboff, P. A. (1996) · Cladistics · doi:10.1006/clad.1996.0015 · Cited by 83 · see citing works
Self-citationMETHODS FOR FASTER PARSIMONY ANALYSIS
Goloboff, P. A. (1996) · Cladistics · doi:10.1111/j.1096-0031.1996.tb00009.x · Cited by 83 · see citing works
Self-citationMRL and SuperFine+MRL: new supertree methods
Nguyen, N., Mirarab, S., & Warnow, T. J. (2012) · Algorithms for Molecular Biology · doi:10.1186/1748-7188-7-3 · Cited by 70 · see citing works
Goloboff, P. A., & Pol, D. (2002) · Cladistics · doi:10.1016/s0748-3007(02)00117-2 · Cited by 66 · see citing works
Self-citationGoloboff, P. A., & Pol, D. (2002) · Cladistics · doi:10.1111/j.1096-0031.2002.tb00289.x · Cited by 58 · see citing works
Self-citationGB‐to‐TNT: facilitating creation of matrices from GenBank and diagnosis of results in TNT
Goloboff, P. A., & Catalano, S. A. (2012) · Cladistics · doi:10.1111/j.1096-0031.2012.00400.x · Cited by 41 · see citing works
Self-citationMinority rule supertrees? MRP, Compatibility, and Minimum Flip may display the least frequent groups
Goloboff, P. A. (2005) · Cladistics · doi:10.1111/j.1096-0031.2005.00064.x · Cited by 39 · see citing works
Self-citationQTL/microarray approach using pathway information
Matsuda, H., Taniguchi, Y., & Iwaisaki, H. (2012) · Algorithms for Molecular Biology · doi:10.1186/1748-7188-7-1 · Cited by 30 · see citing works
What is the rationale for ‘Ockham's razor’ (a.k.a. parsimony) in phylogenetic inference?
Kluge, A. G. (2006) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199297306.003.0002 · Cited by 23 · see citing works
RASA Attributes Highly Significant Structure to Randomized Data
Farris, J. S. (2002) · Cladistics · doi:10.1111/j.1096-0031.2002.tb00155.x · Cited by 14 · see citing works
RASA Attributes Highly Significant Structure to Randomized Data
Farris, J. S. (2002) · Cladistics · doi:10.1006/clad.2002.0204 · Cited by 13 · see citing works
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Potential for Powered Flight Neared by Most Close Avialan Relatives, but Few Crossed Its Thresholds
Pei, R., Pittman, M., Goloboff, P. A., Dececchi, T. A., Habib, M. B., Kaye, T. G., Larsson, H. C. E., Norell, M. A., Brusatte, S. L., & Xu, X. (2020) · Current Biology · doi:10.1016/j.cub.2020.06.105 · Cited by 137 · see citing works
“Parsimony and character weighting All of our analyses included implied weighting (XIW) [103], with modifications proposed by [104] that prevent improper inflation of weights due to missing entries (downweighting the weight of characters with missing entries faster).”
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- Authors
- Goloboff, P. A.
- Affiliations
- Consejo Nacional de Investigaciones Científicas y Técnicas (AR)
- Corresponding author
- Goloboff, Pablo A.
- ORCID
- Goloboff, Pablo A.
- Venue
- Cladistics
- Publisher
- Wiley
- Published
- 2013-07-19
- Volume
- 30
- Issue
- 3
- Pages
- 260-272
- ISSN
- 0748-3007 (ISSN-L)
- 1096-0031
- OpenAlex
- W2049003611
- Cited by
- 248
- References
- 27
- Citations by year
- 2026: 26 · 2025: 23 · 2024: 24 · 2023: 22 · 2022: 16 · 2021: 30 · 2020: 25 · 2019: 17 · 2018: 20 · 2017: 19 · 2016: 15 · 2015: 4 · 2014: 6 · 2013: 1
- FWCI
- 3.88
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Cladistics (publishedVersion)
- PubMed (publishedVersion)
- CONICET Digital (CONICET) (submittedVersion, cc-by-nc-sa)
- Funders
- Consejo Nacional de Investigaciones Científicas y Técnicas (201101, PIP 112 201101 00687, PIP 112, PIP 112 201101, 112 201101 00687)
- Fondo para la Investigación Científica y Tecnológica (PICT 01314)
- 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
- implied weighting, TNT, character weighting, homoplasy, missing data, weight functions, phylogenetic analysis
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