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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

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

Goal

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

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

References

  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. 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. 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: 475–505. 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. 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. 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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