Land plant evolutionary timeline: Gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates

Magallón, Susana; Hilu, Khidir W.; Quandt, Dietmar

doi:10.3732/ajb.1200416

Cited by 291 publications

(326 citation statements)

References 85 publications

(171 reference statements)

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“…To include a full sample of vascular plants (Tracheophyta), Lycopodiophyta were also included. In the fi nal analyses (Magallón et al, 2013), the three living non-vascular lineages, namely liverworts (Marchatiophyta), mosses (Bryophyta), and hornworts (Anthocerotophyta) were added. The deepest split within each major land plant clades is represented, allowing the estimation of their stem group and crown group age.…”

Section: Methodsmentioning

confidence: 99%

“…Sequences were obtained following conventional PCR and sequencing protocols described in Magallón andSanderson (2002, 2005), or downloaded from GenBank. Subsequently, to evaluate the effect of data with different rates of molecular substitution in dating analyses, matK, with a higher rate of substitution, was included (Magallón et al, 2013). The sequences of matK were obtained with protocols described by Wicke and Quandt (2009) and Worberg et al (2007), or obtained from GenBank.…”

Section: Methodsmentioning

confidence: 99%

“…These studies include differential taxonomic sampling and density, are based on different types of data and implement different calibrations and constraints, hence, it not possible to jointly examine the effect of individual parameters on angiosperm age estimates. However, some studies have evaluated the effect of calibration and constraints (Soltis et al, 2002;Moore et al, 2007;Bell et al, 2010;Smith et al, 2010;Clarke et al, 2011;Magallón et al, 2013) the use of different codon positions (Sanderson and Doyle, 2001;Magallón and Sanderson, 2005;Magallón et al, 2013); of different methods to estimate branch lengths (Soltis et al, 2002;Magallón, 2010), and of different relaxed clock method (Magallón, 2010;Magallón et al, 2013).…”

mentioning

confidence: 99%

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

Magallón

2014

Bot. Sci.

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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 ...

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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

Magallón

2014

Bot. Sci.

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“…The central heat map shows annotations for 'conserved' miRNA families, which are here defined as those annotated in at least two of the eight groups, and which have at least one high-confidence annotation. The bottom cladogram illustrates the approximate divergence times (based on (Magallón et al, 2013) and (Wang et al, 2009 …”

Section: Prospectsmentioning

confidence: 99%

Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data

2018

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MicroRNAs (miRNAs) are ~21 nucleotide-long regulatory RNAs that arise from endonucleolytic processing of hairpin precursors. Many function as essential post-transcriptional regulators of target mRNAs and long non-coding RNAs. Alongside miRNAs, plants also produce large numbers of short interfering RNAs (siRNAs), which are distinguished from miRNAs primarily by their biogenesis (typically processed from long double-stranded RNA instead of single-stranded hairpins) and functions (typically via roles in transcriptional regulation instead of posttranscriptional regulation). Next-generation DNA sequencing methods have yielded extensive datasets of plant small RNAs, resulting in many miRNA annotations. However, it has become clear that many miRNA annotations are questionable. The sheer number of endogenous siRNAs compared to miRNAs has been a major factor in the erroneous annotation of siRNAs as miRNAs. Here, we provide updated criteria for the confident annotation of plant miRNAs, suitable for the era of "big data" from DNA sequencing. The updated criteria emphasize replication, the minimization of false positives, and they require next-generation sequencing of small RNAs. We argue that improved annotation systems are needed for miRNAs and all other classes of plant small RNAs. Finally, to illustrate the complexities of miRNA and siRNA annotation, we review the evolution and functions of miRNAs and siRNAs in plants.

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“…Angiosperms originated shortly before the ∼125 Ma origin of the eudicots (62)(63)(64)(65). Hawkmoth adults are mostly dependent on floral resources from eudicots, and the majority of hawkmoth larvae rely on angiosperms as food plants (19).…”

Section: Divergence Time Estimationmentioning

confidence: 99%

Tempo and mode of antibat ultrasound production and sonar jamming in the diverse hawkmoth radiation

Kawahara

Barber

2015

Proc. Natl. Acad. Sci. U.S.A.

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The bat-moth arms race has existed for over 60 million y, with moths evolving ultrasonically sensitive ears and ultrasound-producing organs to combat bat predation. The evolution of these defenses has never been thoroughly examined because of limitations in simultaneously conducting behavioral and phylogenetic analyses across an entire group. Hawkmoths include >1,500 species worldwide, some of which produce ultrasound using genital stridulatory structures. However, the function and evolution of this behavior remain largely unknown. We built a comprehensive behavioral dataset of hawkmoth hearing and ultrasonic reply to sonar attack using high-throughput field assays. Nearly half of the species tested (57 of 124 species) produced ultrasound to tactile stimulation or playback of bat echolocation attack. To test the function of ultrasound, we pitted big brown bats (Eptesicus fuscus) against hawkmoths over multiple nights and show that hawkmoths jam bat sonar. Ultrasound production was immediately and consistently effective at thwarting attack and bats regularly performed catching behavior without capturing moths. We also constructed a fossil-calibrated, multigene phylogeny to study the evolutionary history and divergence times of these antibat strategies across the entire family. We show that ultrasound production arose in multiple groups, starting in the late Oligocene (∼26 Ma) after the emergence of insectivorous bats. Sonar jamming and bat-detecting ears arose twice, independently, in the Miocene (18-14 Ma) either from earless hawkmoths that produced ultrasound in response to physical contact only, or from species that did not respond to touch or bat echolocation attack.acoustic | antipredator defense | bat-moth interactions | evolution | Sphingidae

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Land plant evolutionary timeline: Gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates

Cited by 291 publications

References 85 publications

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

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

Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data

Tempo and mode of antibat ultrasound production and sonar jamming in the diverse hawkmoth radiation

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