Biology:Phylogenetic signal

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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. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 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. ↑ 2.0 2.1 2.2 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. PMID 12778543. https://www.jstor.org/stable/3094610. 
  3. ↑ 3.0 3.1 3.2 3.3 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. http://dx.doi.org/10.1080/10635150802302427. 
  4. ↑ 4.0 4.1 4.2 4.3 4.4 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. 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" (in English). Frontiers in Microbiology 5: 532. doi:10.3389/fmicb.2014.00532. ISSN 1664-302X. PMID 25368606. 
  7. ↑ 7.0 7.1 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. PMID 25780554. PMC 4358766. http://dx.doi.org/10.1111/2041-210x.12293. 
  8. ↑ Felsenstein, Joseph (1985). "Phylogenies and the Comparative Method". The American Naturalist 125 (1): 1–15. doi:10.1086/284325. ISSN 0003-0147. https://www.jstor.org/stable/2461605. 
  9. ↑ 9.0 9.1 9.2 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. https://www.jstor.org/stable/3069271. 
  11. ↑ "Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species | Request PDF" (in en). https://www.researchgate.net/publication/23143538. 
  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" (in en). Nature 470 (7335): 531–534. doi:10.1038/nature09705. ISSN 1476-4687. PMID 21326204. Bibcode: 2011Natur.470..531T. https://www.nature.com/articles/nature09705. 
  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" (in en). Genetics and Molecular Biology 35 (3): 673–679. doi:10.1590/S1415-47572012005000053. ISSN 1415-4757. 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" (in en). Global Ecology and Conservation 27: e01543. doi:10.1016/j.gecco.2021.e01543. ISSN 2351-9894. 
  15. ↑ 15.0 15.1 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. PMID 19843698. 
  16. ↑ Abouheif, E. (1999) (in en). A method for testing the assumption of phylogenetic independence in comparative data. 
  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. PMID 20184650. https://www.jstor.org/stable/40864204. 
  18. ↑ Moran, P. A. P. (1950). "Notes on Continuous Stochastic Phenomena". Biometrika 37 (1/2): 17–23. doi:10.2307/2332142. ISSN 0006-3444. PMID 15420245. http://dx.doi.org/10.2307/2332142. 
  19. ↑ Pagel, Mark (1999). "Inferring the historical patterns of biological evolution". Nature 401 (6756): 877–884. doi:10.1038/44766. ISSN 0028-0836. PMID 10553904. Bibcode: 1999Natur.401..877P. http://dx.doi.org/10.1038/44766. 



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