Phylogenetic signal

The phylogenetic tree above shows significant phylogenetic signal in the mimicry structure of the community. This display confirms closely related species share color patterns more often than expected at random.

Phylogenetic signal is an evolutionary and ecological term, that describes the tendency or the pattern of related biological species to resemble each other more than any other species that is randomly picked from the same phylogenetic tree.[1][2]

## Characteristics

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Phylogenetic signal is usually described as the tendency of related biological species to resemble each other more than any other species that is randomly picked from the same phylogenetic tree.[1][2] In other words, phylogenetic signal can be defined as the statistical dependence among species' trait values that is a consequence of their phylogenetic relationships.[3] The traits (e.g. morphological, ecological, life-history or behavioural traits) are inherited characteristics[4] – meaning the trait values are usually alike within closely related species, while trait values of distantly related biological species do not resemble each other to a such great degree.[5] It is often said that traits that are more similar in closely related taxa than in distant relatives exhibit greater phylogenetic signal. On the other hand, some traits are a consequence of convergent evolution and appear more similar in distantly related taxa than in relatives. Such traits show lower phylogenetic signal.[4]

Phylogenetic signal is a measure, closely related with an evolutionary process and development of taxa. It is thought that high rate of evolution leads to low phylogenetic signal and vice versa (hence, high phylogenetic signal is usually a consequence of either low rate of evolution either stabilizing type of selection).[3] Similarly high value of phylogenetic signal results in an existence of similar traits between closely related biological species, while increasing evolutionary distance between related species leads to decrease in similarity.[4] With a help of phylogenetic signal we can quantify to what degree closely related biological taxa share similar traits.[6]

On the other hand, some authors advise against such interpretations (the ones based on estimates of phylogenetic signal) of evolutionary rate and process. While studying simple models for quantitative trait evolution, such as the homogeneous rate genetic drift, it appears to be no relation between phylogenetic signal and rate of evolution. Within other models (e.g. functional constraint, fluctuating selection, phylogenetic niche conservatism, evolutionary heterogeneity etc.) relations between evolutionary rate, evolutionary process and phylogenetic signal are more complex, and can not be easily generalized using mentioned perception of the relation between two phenomenons.[3] Some authors argue that phylogenetic signal is not always strong in each clade and for each trait. It is also not clear if all of the possible traits do exhibit phylogenetic signal and if it is measurable.[4]

## Aim and methodology

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### Goal

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Phylogenetic signal is a concept widely used in different ecological and evolutionary studies.[7]

Among many questions that can be answered using a concept of phylogenetic signal, the most common ones are:[1]

* To what degree are investigated traits in correlation?[8]
* How, when and why do certain traits evolve?[9]
* Which processes are the driving force of community assembly?[10]
* Do niches get conserved along phylogenies?[11]
* Is there any relation between vulnerability to climate change and taxa phylogeny?[12]

### Techniques

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Quantifying phylogenetic signal can be done using a range of various methods that are used for researching biodiversity in an aspect of evolutionary relatedness. With a help of measuring phylogenetic signal one can determine exactly how studied traits are correlated with phylogenetic relationship between species.[4]

Some of the earliest ways of quantifying phylogenetic signal were based on the use of various statistical methods (such as phylogenetic autocorrelation coefficients, phylogenetic correlograms, as well as autoregressive models). With a help of the mentioned methods one is able to quantify the value of phylogenetic autocorrelation for a studied trait throughout the phylogeny.[13] Another method commonly used in studying phylogenetic signal is so-called Brownian diffusion model of trait evolution that is based on the Brownian motion (BM) principle.[7][14] Using Brownian diffusion model, one can not only study values but also compare those measures between various phylogenies.[1] Phylogenetic signal in continuous traits can be quantified and measured using K-statistic.[3][15] Within this technique values from zero to infinity are used and higher value also means greater level of phylogenetic signal.[15]

The table below shows the most common indices and associated tests used for analyzing phylogenetic signal.[1]

Analyzing phylogenetic signal[1][9] Type of statistics  | Approach  | Based on the model?  | Statistical framework/applied test  | Data  | Reference

|
|
|
|
|

Abouheif's C mean  | Autocorrelation  | X  | Permutation  | Continuous  | [16]
Blomberg's K | Evolutionary  | ✓  | Permutation | Continuous  | [2]
D statistic  | Evolutionary  | ✓  | Permutation  | Categorical  | [17]
Moran's I | Autocorrelation  | X  | Permutation  | Continuous  | [18]
Pagel's λ | Evolutionary  | ✓  | Maximum likelihood | Continuous  | [19]
δstatistic  | Evolutionary  | ✓  | Bayesian  | Categorical  | [9]

## See also

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* Phylogenetic niche conservatism
* Phylogenetic comparative methods

## References

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1. ^ a b c d e f Münkemüller, Tamara; Lavergne, Sébastien; Bzeznik, Bruno; Dray, Stéphane; Jombart, Thibaut; Schiffers, Katja; Thuiller, Wilfried (2012-04-10). "How to measure and test phylogenetic signal". Methods in Ecology and Evolution. 3 (4): 743–756\. Bibcode:2012MEcEv...3..743M. doi:10.1111/j.2041-210x.2012.00196.x. ISSN 2041-210X.
2. ^ a b c Blomberg, Simon P.; Garland, Theodore; Ives, Anthony R. (2003). "Testing for Phylogenetic Signal in Comparative Data: Behavioral Traits Are More Labile". Evolution. 57 (4): 717–745\. doi:10.1111/j.0014-3820.2003.tb00285.x. ISSN 0014-3820. JSTOR 3094610. PMID 12778543. S2CID 221735844.
3. ^ a b c d Revell, Liam J.; Harmon, Luke J.; Collar, David C. (2008-08-01). "Phylogenetic Signal, Evolutionary Process, and Rate". Systematic Biology. 57 (4): 591–601\. doi:10.1080/10635150802302427. ISSN 1076-836X. PMID 18709597. S2CID 2232680.
4. ^ a b c d e Kamilar, Jason M.; Cooper, Natalie (2013-05-19). "Phylogenetic signal in primate behaviour, ecology and life history". Philosophical Transactions of the Royal Society B: Biological Sciences. 368 (1618). doi:10.1098/rstb.2012.0341. ISSN 0962-8436. PMC 3638444. PMID 23569289.
5. ^ Pavoine, Sandrine; Ricotta, Carlo (2012-11-06). "Testing for Phylogenetic Signal in Biological Traits: The Ubiquity of Cross-Product Statistics". Evolution. 67 (3): 828–840\. doi:10.1111/j.1558-5646.2012.01823.x. ISSN 0014-3820. PMID 23461331.
6. ^ Easson, Cole G.; Thacker, Robert W. (2014). "Phylogenetic signal in the community structure of host-specific microbiomes of tropical marine sponges". Frontiers in Microbiology. 5: 532. doi:10.3389/fmicb.2014.00532. ISSN 1664-302X. PMC 4201110. PMID 25368606.
7. ^ a b Vrancken, Bram; Lemey, Philippe; Rambaut, Andrew; Bedford, Trevor; Longdon, Ben; Günthard, Huldrych F.; Suchard, Marc A. (2014-11-13). "Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: applications to viral and host phenotypic evolution". Methods in Ecology and Evolution. 6 (1): 67–82\. doi:10.1111/2041-210x.12293. ISSN 2041-210X. PMC 4358766. PMID 25780554.
8. ^ Felsenstein, Joseph (1985). "Phylogenies and the Comparative Method". The American Naturalist. 125 (1): 1–15\. Bibcode:1985ANat..125....1F. doi:10.1086/284325. ISSN 0003-0147. JSTOR 2461605. S2CID 9731499.
9. ^ a b c Borges, Rui; Machado, João Paulo; Gomes, Cidália; Rocha, Ana Paula; Antunes, Agostinho (2019-06-01). "Measuring phylogenetic signal between categorical traits and phylogenies". Bioinformatics. 35 (11): 1862–1869\. doi:10.1093/bioinformatics/bty800. ISSN 1367-4803. PMID 30358816.
10. ^ Webb, Campbell O.; Ackerly, David D.; McPeek, Mark A.; Donoghue, Michael J. (2002). "Phylogenies and Community Ecology". Annual Review of Ecology and Systematics. 33 (1): 475–505\. Bibcode:2002AnRES..33..475W. doi:10.1146/annurev.ecolsys.33.010802.150448. ISSN 0066-4162. JSTOR 3069271. S2CID 535590.
11. ^ "Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species | Request PDF". ResearchGate. Retrieved 2021-08-30.
12. ^ Thuiller, Wilfried; Lavergne, Sébastien; Roquet, Cristina; Boulangeat, Isabelle; Lafourcade, Bruno; Araujo, Miguel B. (2011). "Consequences of climate change on the tree of life in Europe". Nature. 470 (7335): 531–534\. Bibcode:2011Natur.470..531T. doi:10.1038/nature09705. ISSN 1476-4687. PMID 21326204. S2CID 4406120.
13. ^ Diniz-Filho, José Alexandre F.; Santos, Thiago; Rangel, Thiago Fernando; Bini, Luis Mauricio (2012). "A comparison of metrics for estimating phylogenetic signal under alternative evolutionary models". Genetics and Molecular Biology. 35 (3): 673–679\. doi:10.1590/S1415-47572012005000053. ISSN 1415-4757. PMC 3459419. PMID 23055808.
14. ^ Li, Danfeng; Du, Yanjun; Xu, Wubing; Peng, Danxiao; Primack, Richard; Chen, Guoke; Mao, Ling Feng; Ma, Keping (2021-06-01). "Phylogenetic conservatism of fruit development time in Chinese angiosperms and the phylogenetic and climatic correlates". Global Ecology and Conservation. 27: e01543. Bibcode:2021GEcoC..2701543L. doi:10.1016/j.gecco.2021.e01543. ISSN 2351-9894.
15. ^ a b Ackerly, David (2009-11-17). "Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal". Proceedings of the National Academy of Sciences. 106 (Supplement 2): 19699–19706\. doi:10.1073/pnas.0901635106. PMC 2780941. PMID 19843698.
16. ^ Abouheif, E. (1999). "A method for testing the assumption of phylogenetic independence in comparative data". S2CID 14934629. `{{cite journal}}`: Cite journal requires `|journal=` (help)
17. ^ FRITZ, SUSANNE A.; PURVIS, ANDY (2010). "Selectivity in Mammalian Extinction Risk and Threat Types: a New Measure of Phylogenetic Signal Strength in Binary Traits". Conservation Biology. 24 (4): 1042–1051\. Bibcode:2010ConBi..24.1042F. doi:10.1111/j.1523-1739.2010.01455.x. ISSN 0888-8892. JSTOR 40864204. PMID 20184650. S2CID 29107177.
18. ^ Moran, P. A. P. (1950). "Notes on Continuous Stochastic Phenomena". Biometrika. 37 (1/2): 17–23\. doi:10.2307/2332142. ISSN 0006-3444. JSTOR 2332142. PMID 15420245.
19. ^ Pagel, Mark (1999). "Inferring the historical patterns of biological evolution". Nature. 401 (6756): 877–884\. Bibcode:1999Natur.401..877P. doi:10.1038/44766. ISSN 0028-0836. PMID 10553904. S2CID 205034365.

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Phylogenetics

Relevant fields|

* Computational phylogenetics
* Molecular phylogenetics
* Cladistics
* Taxonomy
* Evolutionary taxonomy
* Systematics

* Evolutionary biology portal

Basic concepts|

* Phylogenesis
* Cladogenesis
* Phylogenetic tree
* Cladogram
* Phylogenetic network
* Long branch attraction
* Clade vs Grade
* Lineage
* Ghost lineage
* Ghost population

Inference methods|

* Maximum parsimony
* Phylogenetic reconciliation
* Probabilistic methods
* Maximum likelihood
* Bayesian inference
* Distance-matrix methods
* Neighbor-joining
* UPGMA
* Least squares
* Three-taxon analysis

Current topics|

* PhyloCode
* DNA barcoding
* Molecular phylogenetics
* Phylogenetic comparative methods
* Phylogenetic niche conservatism
* Phylogenetic signal
* Phylogenetics software
* Phylogenomics
* Phylogeography

Group traits|

* Primitive
* Plesiomorphy
* Symplesiomorphy
* Derived
* Apomorphy
* Synapomorphy
* Autapomorphy

Group types|

* Monophyly
* Paraphyly
* Polyphyly

Nomenclature|

* Phylogenetic nomenclature
* Crown group
* Sister group
* Basal
* Supertree

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