A Time-Calibrated Road Map of Brassicaceae Species Radiation and Evolutionary History

Abstract

The Brassicaceae include several major crop plants and numerous important model species in comparative evolutionary research such as Arabidopsis, Brassica, Boechera, Thellungiella, and Arabis species. As any evolutionary hypothesis needs to be placed in a temporal context, reliably dated major splits within the evolution of Brassicaceae are essential. We present a comprehensive time-calibrated framework with important divergence time estimates based on whole-chloroplast sequence data for 29 Brassicaceae species. Diversification of the Brassicaceae crown group started at the Eocene-to-Oligocene transition. Subsequent major evolutionary splits are dated to ;20 million years ago, coinciding with the Oligocene-toMiocene transition, with increasing drought and aridity and transient glaciation events. The age of the Arabidopsis thaliana crown group is 6 million years ago, at the Miocene and Pliocene border. The overall species richness of the family is well explained by high levels of neopolyploidy (43% in total), but this trend is neither directly associated with an increase in genome size nor is there a general lineage-specific constraint. Our results highlight polyploidization as an important source for generating new evolutionary lineages adapted to changing environments. We conclude that species radiation, paralleled by high levels of neopolyploidization, follows genome size decrease, stabilization, and genetic diploidization.

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

“…At the level of individual gene trees (Supplementary Fig. 3), 100% supported the monophyly of A. thaliana-as expected, given that this species is estimated to have diverged from the rest of the genus at least 6 million years ago (Myr) 9 ( Supplementary Fig. 4) and is reproductively isolated as a consequence of a chromosome number of 5 rather than 8 ( Table 1).…”

“…Owing to the lack of fossils from the genus Arabidopsis or the Brassicaceae family we used secondary calibration for divergence time estimation. Three calibration points were extracted from Hohmann et al 9 : The age of the outgroup (split between the genera Camelina and Capsella) was set to 7.3572 Myr; the crown age of the genus Arabidopsis was set to 5.9685 Myr, and the root height (split between outgroup and genus Arabidopsis) was set to 8.1627 Myr. Normal distributions with a s.d.…”

“…Normal distributions with a s.d. = 1.0 fit the 95% confidence intervals from Hohmann et al 9 and were thus used for all three calibration points. An additional constraint was set on the root height by truncation to 4-12 Myr.…”

Comparative genomics and trait evolution in Cleomaceae, a model family for ancient polyploidy

“…The At-β event, which occurred approximately 56 Ma (Kagale et al, 2014) and is shared by Brassicaceae, including its earliest split sister group Aethionema arabicum (Haudry et al, 2013) seems to correlate with chain elongation of Met-derived GS (Schranz et al, 2011). Additionally, speciation rate shifts have been observed that are consistent with the estimated age of that polyploid event (Franzke et al, 2011;Hohmann et al, 2015). Detection and rough dating of these polyploid events are mostly dependent on calculation of synonymous substitution rates (Ks).…”

From species to trait evolution in Aethionema (Brassicaceae)

“…The entire Brassicaceae shares a common whole genome duplication event referred to as At-alpha , Haudry et al 2013. Brassicaceae are globally distributed over the temperate regions (Hohmann et al 2015) and contain species that are metal-tolerant (e.g. Noccaea caerulescens), salt tolerant (e.g.…”