Diversification in clonal and nonclonal species

• Thesis title in Czech: Diverzifikace u klonálních a neklonálních rostlin
• Thesis title in English: Diversification in clonal and nonclonal species
• English key words: Diversification in clonal and nonclonal species
• Academic year of topic announcement: 2022/2023
• Thesis type: dissertation
• Thesis language: angličtina
• Department: Department of Botany (31-120)
• Supervisor: prof. RNDr. Tomáš Herben, CSc.
• Author: hidden - assigned by the advisor
• Date of registration: 10.10.2022
• Date of assignment: 13.10.2022
• Advisors: Mgr. Jan Smyčka, Ph.D.

References

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Beaulieu JM, O’Meara BC. 2016. Detecting hidden diversification shifts in models of trait-dependent speciation and extinction, Syst Biol 65: 583–601.
Bolker BM. et al. 2009. Generalized linear mixed models: a practical guide for ecology and evolution. Trends Ecol Evol 24: 127-135.
Eriksson O. 1992. Evolution of seed dispersal and recruitment in clonal plants. Oikos 63: 439-448
FitzJohn RG 2009. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Syst Biol 58, 595–611.
Herben T, Klimešová J 2020. Evolution of clonal growth forms in angiosperms. New Phytol 225: 999–1010.
Herrera-Alsina L. et al. 2019. Detecting the dependence of diversification on multiple traits from phylogenetic trees and trait data. Syst Biol 68: 317–328.
Ho, L. S. T. & Ané, C. (2014) A linear-time algorithm for gaussian and non-gaussian trait evolution models. Syst. Biol. 63, 397–408.
Janovský Z, Herben T. 2020. Reaching similar goals by different means - Differences in life-history strategies of clonal and non-clonal plants. Perspect Plant Ecol Evol Syst 44: 125534.
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Kattge J. et al. 2020. TRY plant trait database – enhanced coverage and open access. Glob Change Biol 26, 119–188.
Klimešová J. et al. 2017. CLO-PLA: a database of clonal and bud-bank traits of the Central European flora. Ecology 98, 1179.
Klimešová J., Ottaviani G., Charles-Dominique T., Campetella G., Canullo R., Chelli S., Janovský Z., Lubbe F. C., Martínková J. and Herben T. (2021) Incorporating clonality into the plant ecology research agenda. Trends in Plant Science 26: 1236-1247. doi: 10.1016/j.tplants.2021.07.019
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Maliet O., Hartig F. and Morlon H. 2019, A model with many small shifts for estimating species-specific diversificaton rates, Nature Ecology and Evolution, doi 10.1038/s41559-019-0908-0
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Preliminary scope of work

The main task of the PhD. student will be to test the following two hypotheses:
Diversification rates in predominantly clonal plant lineages differ from the rates in predominantly non-clonal lineages. To test this, they will assemble and analyze data on evolutionary dynamics of clonality on large phylogenetic scales from existing databases and link them with phylogenetic data using likelihood-based State-dependent Speciation Extinction (SSE) models.
Rates of molecular evolution are slower in lineages with prevailing share of clonal species. This will be tested with pairs of higher taxa covering the whole variability in clonality trait difference identified using the ancestral state estimations from the SSE models. These pairs will be used to infer the relationship between clonality status and the rate of molecular evolution in different types of regions (nuclear and chloroplast, coding vs non-coding, and synonymous vs non-synonymous).

Preliminary scope of work in English

The main task of the PhD. student will be to test the following two hypotheses:
Diversification rates in predominantly clonal plant lineages differ from the rates in predominantly non-clonal lineages. To test this, they will assemble and analyze data on evolutionary dynamics of clonality on large phylogenetic scales from existing databases and link them with phylogenetic data using likelihood-based State-dependent Speciation Extinction (SSE) models.
Rates of molecular evolution are slower in lineages with prevailing share of clonal species. This will be tested with pairs of higher taxa covering the whole variability in clonality trait difference identified using the ancestral state estimations from the SSE models. These pairs will be used to infer the relationship between clonality status and the rate of molecular evolution in different types of regions (nuclear and chloroplast, coding vs non-coding, and synonymous vs non-synonymous).