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Seeing the forest for the trees: the limitations of phylogenies in comparative biology: (American Society of Naturalists Address)

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Losos, Jonathan B.·2011·The American Naturalist
DOI 10.1086/660020
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Abstract

The past 30 years have seen a revolution in comparative biology. Before that time, systematics was not at the forefront of the biological sciences, and few scientists considered phylogenetic relationships when investigating evolutionary questions. By contrast, systematic biology is now one of the most vigorous disciplines in biology, and the use of phylogenies not only is requisite in macroevolutionary studies but also has been applied to a wide range of topics and fields that no one could possibly have envisioned 30 years ago. My message is simple: phylogenies are fundamental to comparative biology, but they are not the be-all and end-all. Phylogenies are powerful tools for understanding the past, but like any tool, they have their limitations. In addition, phylogenies are much more informative about pattern than they are about process. The best way to fully understand the past-both pattern and process-is to integrate phylogenies with other types of historical data as well as with direct studies of evolutionary process.

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  • The problem of species non-independence still arises when examining evolutionary labile traits that evolve very fast or are the product of very recent events.

    “The problem of species non-independence still arises when examining evolutionary labile traits that evolve very fast or are the product of very recent events.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [54]

    In “Many Traits in Many Clades Do Not Exhibit Phylogenetic Effect” (page unavailable), Losos says rapid evolutionary change can leave closely related species phenotypically dissimilar. The same section says that when a trait lacks phylogenetic effect, values in closely related species may be statistically independent—the contrary of the claim that non-independence still arises for such traits. (LLM, conf=0.88)

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  • This fundamental problem has sown doubts about the suitability and reliability of many methods in comparative biology.

    “This fundamental problem has sown doubts about the suitability and reliability of many methods in comparative biology (e.g., Losos 2011), even if it was not obvious that these issues were connected.”

    From Rethinking phylogenetic comparative methods (2018) · cites this paper as Losos 2011

  • A total lack of phylogenetic signal is at one end of a spectrum and not a reason not to avoid phylogenetic comparative methods.

    “A total lack of phylogenetic signal is at one end of a spectrum and not a reason not to avoid phylogenetic comparative methods44,54–56.”

    From A phylogenetic approach to comparative genomics (2025) · cites this paper as [54]

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Authors
Losos, J. B.
Affiliations
Harvard University (US)
Corresponding author
Losos, Jonathan B.
ORCID
Losos, Jonathan B.
Venue
The American Naturalist
Publisher
University of Chicago Press
Published
2011-06
Volume
177
Issue
6
Pages
709-727
ISSN
  • 0003-0147 (ISSN-L)
  • 1537-5323
DOI
10.1086/660020
OpenAlex
W1867898441
Cited by
284
References
4
Citations by year
2026: 4 · 2025: 14 · 2024: 27 · 2023: 11 · 2022: 18 · 2021: 12 · 2020: 10 · 2019: 17 · 2018: 15 · 2017: 14 · 2016: 17 · 2015: 26 · 2014: 33 · 2013: 32 · 2012: 28
FWCI
19.99
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • The American Naturalist (publishedVersion)
  • PubMed (publishedVersion)
  • Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
Topics
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
Keywords
phylogeny, comparative biology, phylogenetic systematics, macroevolution, evolutionary processes, historical data
MeSH terms
Biology, Biological Evolution, Phylogeny, History, 20th Century, History, 21st Century

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