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Speciation rate
Leščinskij, Artem ; Storch, David (advisor) ; Macháč, Antonín (referee)
Speciation rate is a frequency at which an original species splits into two species per unit of time. Since this rate cannot be directly determined, it must be inferred from the fossil record or a reconstructed phylogeny using appropriate diversification model or nodes and branches of a phylogenetic tree. The homogeneous birth-death process is the basic method upon which other models, such as time-dependent or density-dependent models, are based. Non-model methods such as DR statistics, node-density metrics or inverstion length of terminal branches, are methods depend on reconstructed phylogenetic trees. More complex methods include MEDUSA, BAMM, CLaDS, MTBD, or trait-dependant models. Protracted-speciation models are biologically more plausible and describe speciation as a gradual process. These methods can detect more complex diversification regimes. Tip rate determines expected species-specific rate of speciation and is less dependent on the rates of extinction and diversification; rather, it corresponds to the rate of speciation. Model identifiability is a fundamental problem limiting the estimation of the speciation rate, but this limitation can be partially overcome by new techniques such as pulled rates. Keywords: speciation rate, phylogeny, diversification, evolution, model
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Diversity dynamics across scales
Macháč, Antonín ; Storch, David (advisor) ; Remeš, Vladimír (referee) ; Ricklefs, Robert (referee)
Charles University, Prague Diversity dynamics across scales Antonin Machac 2018 Abstract Diversity dynamics remain controversial. It has been suggested that the dynamics are expansionary, such that the number of species across regions and clades increases constantly. However, the opposite has also been suggested, namely that species numbers are relatively stable, following equilibrial dynamics. Both views (expansionary and equilibrial) have been supported by compelling phylogenetic, biogeographic, and fossil evidence and, currently, it remains largely unclear how the two seemingly conflicting views could be reconciled. My dissertation addresses this question, based on the premise that diversity dynamics change systematically with scale. Specifically, I hypothesize that expansionary dynamics typify regionally distributed, small, and young clades whose diversity tends to expand, driven by a variety of regionally relevant factors (e.g. habitat-level adaptation, biotic interactions, or montane shifts leading to ecological divergence and speciation). Conversely, equilibrial dynamics typify large, ancient, and globally distributed clades, whose diversity is environmentally limited (e.g. by the total amount of resources that can sustain only a limited number of populations and species). Consequently, it seems...
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Diversity dynamics across scales
Macháč, Antonín ; Storch, David (advisor) ; Remeš, Vladimír (referee) ; Ricklefs, Robert (referee)
Charles University, Prague Diversity dynamics across scales Antonin Machac 2018 Abstract Diversity dynamics remain controversial. It has been suggested that the dynamics are expansionary, such that the number of species across regions and clades increases constantly. However, the opposite has also been suggested, namely that species numbers are relatively stable, following equilibrial dynamics. Both views (expansionary and equilibrial) have been supported by compelling phylogenetic, biogeographic, and fossil evidence and, currently, it remains largely unclear how the two seemingly conflicting views could be reconciled. My dissertation addresses this question, based on the premise that diversity dynamics change systematically with scale. Specifically, I hypothesize that expansionary dynamics typify regionally distributed, small, and young clades whose diversity tends to expand, driven by a variety of regionally relevant factors (e.g. habitat-level adaptation, biotic interactions, or montane shifts leading to ecological divergence and speciation). Conversely, equilibrial dynamics typify large, ancient, and globally distributed clades, whose diversity is environmentally limited (e.g. by the total amount of resources that can sustain only a limited number of populations and species). Consequently, it seems...
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