Diversification in clonal and nonclonal species

• Název práce v češtině: Diverzifikace u klonálních a neklonálních rostlin
• Název v anglickém jazyce: Diversification in clonal and nonclonal species
• Klíčová slova anglicky: Diversification in clonal and nonclonal species
• Akademický rok vypsání: 2022/2023
• Typ práce: disertační práce
• Jazyk práce: angličtina
• Ústav: Katedra botaniky (31-120)
• Vedoucí / školitel: prof. RNDr. Tomáš Herben, CSc.
• Řešitel: skrytý - zadáno vedoucím/školitelem
• Datum přihlášení: 10.10.2022
• Datum zadání: 13.10.2022
• Konzultanti: Mgr. Jan Smyčka, Ph.D.

Seznam odborné literatury

Arnaud-Haond S. et al. 2007. Standardizing methods to address clonality in population studies. Mol Ecol 16: 5115-5139.
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.
Jetz, W., Thomas, G. H., Joy, J. B., Hartmann, K. & Mooers, A. O. (2012) The global diversity of birds in space and time. Nature491, 444–448.
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
Lanfear R. 2013. Taller plants have lower rates of molecular evolution. Nature. Comm 4: 1879.
Lanfear R. et al. 2010. Watching the clock: studying variation in rates of molecular evolution between species. Trends Ecol Evol 25: 495-503.
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
O’Meara BC. 2016. Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity. Proc Roy Soc B 283: 20152304.
Pond SLK 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676–679.
Rabosky, D. L. Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PLoS One9, (2014).
Rabosky D.L. & Goldberg EE. 2015. Model inadequacy and mistaken inferences of trait-dependent speciation. Syst. Biol. 64: 340–355
Roquet C. 2013. Replicated radiations of the alpine genus Androsace (Primulaceae) driven by range expansion and convergent key innovations. J Biog 40: 1874-1886.
Smith SA, Brown JW. 2018. Constructing a broadly inclusive seed plant phylogeny. Am J Bot 105: 302–314.
Vallejo-Marín M et al. 2010. The ecological and evolutionary consequences of clonality for plant mating. Ann Rev Ecol Evol Syst 2010. 41: 193–213.
Van Drunen WE, Husband BC. 2019. Evolutionary associations between polyploidy, clonal reproduction, and perenniality in the angiosperms. New Phytol 224: 1266-1277.
Ye D. et al. 2014. Clonality-climate relationships along latitudinal gradient across China: Adaptation of clonality to environments. Plos One 9: e94009.

Předběžná náplň práce

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).

Předběžná náplň práce v anglickém jazyce

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).