Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology: Concepts and Practice
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Current comparative methods are not designed to deal with abrupt shifts and discontinuities.
“But as recent controversies in phylogenetic comparative biology have highlighted, our current methods (reviewed in O'Meara 2012;Pennell and Harmon 2013;Garamszegi 2014) are not designed to deal with such dynamics.”
From Rethinking phylogenetic comparative methods (2018) · cites this paper as Garamszegi 2014
The problem of non-independence is not solved by alternative methods such as grouping data by a higher taxonomic rank or by downsampling.
“The problem of non-independence is not solved by alternative methods such as grouping data by a higher taxonomic rank (for example, genera or family), or by sampling the same number of genomes from taxonomic groups to minimize oversampling (‘downsampling’)102,103.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [103]
Cites
Phylogenies and the Comparative Method
Felsenstein, J. (1985) · The American Naturalist · doi:10.1086/284325 · Cited by 9,793 · see citing works
The delayed rise of present-day mammals
Bininda-Emonds, O. R. P., Cardillo, M., Jones, K. E., MacPhee, R. D. E., Beck, R. M. D., Grenyer, R., Price, S. A., Vos, R. A., Gittleman, J. L., & Purvis, A. (2007) · Nature · doi:10.1038/nature05634 · Cited by 2,082 · see citing works
A nonparametric approach to estimating divergence times in the absence of rate constancy.
Sanderson, M. J. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025731 · Cited by 1,156 · see citing works
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Rethinking phylogenetic comparative methods
Uyeda, J. C., Zenil-Ferguson, R., & Pennell, M. W. (2018) · Systematic Biology · doi:10.1093/sysbio/syy031 · Cited by 313 · see citing works
Ecological drivers of song evolution in birds: Disentangling the effects of habitat and morphology
Derryberry, E. P., Seddon, N., Derryberry, G. E., Claramunt, S., Seeholzer, G. F., Brumfield, R. T., & Tobias, J. A. (2018) · Ecology and Evolution · doi:10.1002/ece3.3760 · Cited by 120 · see citing works
Comparative bioacoustics: a roadmap for quantifying and comparing animal sounds across diverse taxa
Odom, K. J., Araya‐Salas, M., Morano, J. L., Ligon, R. A., Leighton, G. M., Taff, C. C., Dalziell, A. H., Billings, A. C., Germain, R. R., Pardo, M., et al. (2021) · Biological Reviews · doi:10.1111/brv.12695 · Cited by 81 · see citing works
Grabowski, M., Voje, K. L., & Hansen, T. F. (2016) · Journal of Human Evolution · doi:10.1016/j.jhevol.2016.03.001 · Cited by 55 · see citing works
A phylogenetic approach to comparative genomics
Dewar, A. E., Belcher, L. J., & West, S. A. (2025) · Nature Reviews Genetics · doi:10.1038/s41576-024-00803-0 · Cited by 41 · see citing works
Wartel, A., Lindenfors, P., & Lind, J. (2019) · PLOS ONE · doi:10.1371/journal.pone.0218655 · Cited by 40 · see citing works
- Authors
- Garamszegi, L. Z.
- Affiliations
- Consejo Superior de Investigaciones Científicas (ES)
- Corresponding author
- László Zsolt Garamszegi
- Venue
- Springer eBooks
- Publisher
- Springer Berlin Heidelberg
- Published
- 2014
- OpenAlex
- W2498782314
- Cited by
- 538
- References
- 3
- Citations by year
- 2026: 25 · 2025: 41 · 2024: 29 · 2023: 54 · 2022: 59 · 2021: 62 · 2020: 50 · 2019: 60 · 2018: 47 · 2017: 45 · 2016: 39 · 2015: 26 · 2014: 1
- FWCI
- 22.40
- Type
- book
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Springer eBooks (publishedVersion)
- Thammasat University Digital Collections (submittedVersion)
- TU Digital Collections (Thammasat University) (submittedVersion)
- Digital Access to Libraries (Université catholique de Louvain (UCL), l'Université de Namur (UNamur) and the Université Saint-Louis (USL-B)) (submittedVersion)
- Topics
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Physical Sciences › Mathematics › Geometry and Topology › Morphological variations and asymmetry
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Animal Behavior and Reproduction
- Keywords
- phylogenetic comparative analysis, phylogeny, animal communities, species interactions, evolutionary inference, phylogenetic signal detection
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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.
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