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Analysis of institutional authors

Molina-Venegas RCorresponding Author

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February 11, 2022
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Revisiting phylogenetic signal; strong or negligible impacts of polytomies and branch length information?

Publicated to:BMC EVOLUTIONARY BIOLOGY. 17 (1): 53- - 2017-02-15 17(1), DOI: 10.1186/s12862-017-0898-y

Authors: Molina-Venegas R; Rodríguez M

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Abstract

Background: Inaccurate estimates of phylogenetic signal may mislead interpretations of many ecological and evolutionary processes, and hence understanding where potential sources of uncertainty may lay has become a priority for comparative studies. Importantly, the sensitivity of phylogenetic signal indices and their associated statistical tests to incompletely resolved phylogenies and suboptimal branch-length information has been only partially investigated. Methods: Here, we use simulations of trait evolution along phylogenetic trees to assess whether incompletely resolved phylogenies (polytomic chronograms) and phylogenies with suboptimal branch-length information (pseudo-chronograms) could produce directional biases in significance tests (p-values) associated with Blomberg et al.'s K and Pagel's lambda (λ) statistics, two of the most widely used indices to measure and test phylogenetic signal. Specifically, we conducted pairwise comparisons between the p-values resulted from the use of true chronograms and their degraded counterparts (i.e. polytomic chronograms and pseudo-chronograms), and computed the frequency with which the null hypothesis of no phylogenetic signal was accepted using true chronograms but rejected when using their degraded counterparts (type I bias) and vice versa (type II bias). Results: We found that the use of polytomic chronograms in combination with Blomberg et al.'s K resulted in both, clearly inflated estimates of phylogenetic signal and moderate levels of type I and II biases. More importantly, pseudo-chronograms led to high rates of type I biases. In contrast, Pagel's λ was strongly robust to either incompletely resolved phylogenies and suboptimal branch-length information. Conclusions: Our results suggest that pseudo-chronograms can lead to strong overestimation of phylogenetic signal when using Blomberg et al.'s K (i.e. high rates of type I biases), while polytomies may be a minor concern given other sources of uncertainty. In contrast, Pagel's λ seems strongly robust to either incompletely resolved phylogenies and suboptimal branch-length information. Hence, Pagel's λ may be a more appropriate alternative over Blomberg et al.'s K to measure and test phylogenetic signal in most ecologically relevant traits when phylogenetic information is incomplete.

Keywords

bladjblomberg’s kpagel’s lambdaphylogenetic resolutionphylogeny calibrationBladjBlomberg's kPagel's lambdaPhylogenetic resolutionPhylogeny calibrationPseudo-chronograms

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal BMC EVOLUTIONARY BIOLOGY due to its progression and the good impact it has achieved in recent years, according to the agency Scopus (SJR), it has become a reference in its field. In the year of publication of the work, 2017, it was in position , thus managing to position itself as a Q1 (Primer Cuartil), in the category Ecology, Evolution, Behavior and Systematics. Notably, the journal is positioned above the 90th percentile.

From a relative perspective, and based on the normalized impact indicator calculated from World Citations provided by WoS (ESI, Clarivate), it yields a value for the citation normalization relative to the expected citation rate of: 3.62. This indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: ESI Nov 14, 2024)

This information is reinforced by other indicators of the same type, which, although dynamic over time and dependent on the set of average global citations at the time of their calculation, consistently position the work at some point among the top 50% most cited in its field:

  • Weighted Average of Normalized Impact by the Scopus agency: 6.02 (source consulted: FECYT Feb 2024)
  • Field Citation Ratio (FCR) from Dimensions: 20.59 (source consulted: Dimensions Jul 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-07-18, the following number of citations:

  • WoS: 94
  • Scopus: 109

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-07-18:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 254.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 269 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 9.
  • The number of mentions on the social network X (formerly Twitter): 4 (Altmetric).

Leadership analysis of institutional authors

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (MOLINA VENEGAS, RAFAEL) .

the author responsible for correspondence tasks has been MOLINA VENEGAS, RAFAEL.