A Review of the Effect of Relaxed Clock Method, Long Branches, Genes, and Calibrations in the Estimation of Angiosperm Age

Abstract

Abstract:The timing of angiosperm origin and diversifi cation is crucial to understand the evolution of terrestrial ecosystems as we know them today. The fossil record and relaxed molecular clocks provide substantially different estimates of the time in which angiosperms started to diversify into lineages that originated living species. The roles of different methodological and systematic factors on ages estimated with relaxed clocks across land plants, with a focus on angiosperms, are here reviewed. Different relaxed clocks and molecular data provided similar age estimates for nodes across land plants. Breaking the long branch subtending angiosperms typically did not result in substantially younger age estimates for angiosperms. Including or excluding fossil-derived calibrations on internal nodes had a pronounced effect on ages across the tree, and among examined factors, calibrations were the most infl uential in resulting ages. However, interactions between calibrations and genes were detected as different genes converged on similar ages when the same set of calibrations was applied. Estimated angiosperm ages were much older than angiosperm earliest fossils. Although a missing fossil history cannot be ruled out, this explanation alone is insuffi cient, considering the gradually increasing abundance, diversity and geographical distribution of angiosperms in the fossil record; the ordered progression of their morphological and functional diversifi cation; and the agreement in the sequence of appearance of lineages in the stratigraphic record and in molecular phylogenies. It is hypothesized that model misspecifi cation may play a role in the observed molecular clock/fossil discrepancy. Key words: calibrations, fossil record, land plants, lineage effects, model misspecifi cation.Resumen: La edad del origen y diversifi cación de las angiospermas son cruciales para entender la evolución de los ecosistemas terrestres modernos. El registro fósil y los relojes moleculares relajados calculan edades substancialmente diferentes para el inicio de la diversifi cación de las angiospermas. Se revisa el efecto de diferentes factores metodológicos y sistemáticos en los estimados de relojes relajados para las plantas terrestres, con énfasis en las angiospermas. Diferentes métodos de reloj relajado y datos moleculares estimaron edades similares en todo el árbol fi logenético. Romper la rama larga que subyace a las angiospermas no resultó en edades substancialmente más jóvenes. La inclusión o exclusión de calibraciones derivadas del registro fósil tuvo un efecto pronunciado en las edades estimadas, además de ser el factor más relevante entre los que se evaluaron. Sin embargo, existen interacciones entre las calibraciones y los genes, pues diferentes genes convergieron en edades similares cuando las mismas calibraciones fueron aplicadas. Las edades estimadas para las angiospermas son mucho más viejas que sus primeros fósiles. Aunque la posibilidad de un registro fósil incompleto no puede excluirse, ésta sola explicación es insufi ...

Biases in assessing the evolutionary history of the angiosperm flora of China

“…Most estimates of the crown angiosperm age fall between 150 and 250 Mya (e.g. 149–256 Mya, Barba‐Montoya, Reis, Schneider, Donoghue, & Yang, ; 162–210 Mya, Magallón, ; 175–240 Mya, Clarke, Warnock, & Donoghue, ; 190–238 Mya, Murat, Armero, Pont, Klopp, & Salse, ; 182–257 Mya, Smith, Beaulieu, & Donoghue, ; 192–251 Mya, Foster et al., ; 158–179 Mya, Wikström, Savolainen, & Chase, ; 167–199 Mya, Bell, Soltis, & Soltis, ). Molecular clocks suggest a Triassic age for crown angiosperms (e.g.…”

“…Figure S1 in Supporting Information), suggesting that using a different phylogeny in Lu et al's analysis might yield a substantially different conclusion. Because molecular divergence-time estimates are extremely sensitive to placements of calibrating fossils at crown versus stem nodes and to choices of methods and calibration scenarios (Magallón, 2014;Sauquet et al, 2012;Wilf & Escapa, 2015), it is inappropriate to determine the origination time of a genus, or a taxon at any rank, solely based on molecular date derived from a phylogenetic tree, as in Lu et al (2018) and other studies (e.g. Song & Cui, 2017).…”

Burmese amber fossils bridge the gap in the Cretaceous record of polypod ferns

“…Application of the angiosperm pollen record as a maximum age constraint led to the hypothesis of a Cretaceous origin of the angiosperm crown group whereas a minimum age constraint allows to consider an initial diversification in the Triassic (Schneider et al, 2004;Bell et al, 2010;Smith et al, 2010;Magallón, 2014;Zeng et al, 2014;Magallón et al, 2015). However, node age calibrations are challenged by a range of issues and thus the impact of each fossil must be studied independently.…”

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“…Hence, calculated ages are considerably older than the oldest accepted angiosperm fossils of about 130 mya (Friis et al 2011). The age of the earliest angiosperm lineages remains hotly debated (Buerki et al 2014; Doyle and Endress 2014; Magallón 2014; Beaulieu et al 2015; Magallón et al 2015; Foster et al 2017; Herendeen et al 2017). …”