ArticleMethods in ecology and evolution2016
Shedding light on the 'dark side' of phylogenetic comparative methods.
Article in Methods in ecology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Revisiting the relationship between stomatal size and speed across species - a meta-analysis.The New phytologist · 2026Pooled it
- Functional group classification using consensus clustering.PLoS computational biology · 2026Article
- Multi-response phylogenetic mixed models: concepts and application.Biological reviews of the Cambridge Philosophical Society · 2025Review
- Comparative Analyses and Phylogenetic Dependence in Traits and Trends of the Dipterocarpaceae.Ecology and evolution · 2025Article
- Evolution of the syrinx of Apodiformes, including the vocal-learning Trochilidae (Aves: Strisores).Zoological journal of the Linnean Society · 2024Article
- Breaking the constraint on the number of cervical vertebrae in mammals: On homeotic transformations in lorises and pottos.Evolution & development · 2022Article
- Evolution of sex allocation plasticity in a hermaphroditic flatworm genus.Journal of evolutionary biology · 2022Article
- Four key challenges in the open-data revolution.The Journal of animal ecology · 2021Article
- Plasma methionine metabolic profile is associated with longevity in mammals.Communications biology · 2021Article
- Herbivore-induced defenses are not under phylogenetic constraints in the genusEcology and evolution · 2021Article
- Special Care Is Needed in Applying Phylogenetic Comparative Methods to Gene Trees with Speciation and Duplication Nodes.Molecular biology and evolution · 2021Article
- The Effect of Locomotion Mode on Body Shape Evolution in Teleost Fishes.Integrative organismal biology (Oxford, England) · 2021Article
- Gene expression and regulatory factors of the mechanistic target of rapamycin (mTOR) complex 1 predict mammalian longevity.GeroScience · 2020Article
- Body shape diversification along the benthic-pelagic axis in marine fishes.Proceedings. Biological sciences · 2020Article
- Low abundance of NDUFV2 and NDUFS4 subunits of the hydrophilic complex I domain and VDAC1 predicts mammalian longevity.Redox biology · 2020Article
- Angiosperm speciation cools down in the tropics.Ecology letters · 2020Article
- Habitat transitions alter the adaptive landscape and shape phenotypic evolution in needlefishes (Belonidae).Ecology and evolution · 2020Article
- Article
- Migratory lineages rapidly evolve larger body sizes than non-migratory relatives in ray-finned fishes.Proceedings. Biological sciences · 2020Article
- Tradeoffs in hyphal traits determine mycelium architecture in saprobic fungi.Scientific reports · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phylogenetic comparative methods are becoming increasingly popular for investigating evolutionary patterns and processes. However, these methods are not infallible - they suffer from biases and make assumptions like all other statistical methods.Unfortunately, although these limitations are generally well known in the phylogenetic comparative methods community, they are often inadequately assessed in empirical studies leading to misinterpreted results and poor model fits. Here, we explore reasons for the communication gap dividing those developing new methods and those using them.We suggest that some important pieces of information are missing from the literature and that others are difficult to extract from long, technical papers. We also highlight problems with users jumping straight into software implementations of methods (e.g. in r) that may lack documentation on biases and assumptions that are mentioned in the original papers.To help solve these problems, we make a number of suggestions including providing blog posts or videos to explain new methods in less technical terms, encouraging reproducibility and code sharing, making wiki-style pages summarising the literature on popular methods, more careful consideration and testing of whether a method is appropriate for a given question/data set, increased collaboration, and a shift from publishing purely novel methods to publishing improvements to existing methods and ways of detecting biases or testing model fit. Many of these points are applicable across methods in ecology and evolution, not just phylogenetic comparative methods.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.