Diaz, S. | bioRxiv Science

bioRxiv2018

Two key events associated with a transposable element burst occurred during rice domestication

Transposable elements shape genome evolution through periodic bursts of amplification. In this study we exploited knowledge of the components of the mPing/Ping/Pong TE family in four rice strains undergoing mPing bursts to track their copy numbers and distribution in a large collection of genomes from the wild progenitor Oryza rufipogon and domesticated Oryza sativa (rice). We characterized two events that occurred to the autonomous Ping element and appear to be critical for mPing hyperactivity. First, a point mutation near the end of the element created a Ping variant (Ping16A) with reduced transposition. The proportion of strains with Ping16A has increased during domestication while the original Ping (Ping16G) has been dramatically reduced. Second, transposition of Ping16A into a Stowaway element generated a locus (Ping16A_Stow) whose presence correlates with strains that have high mPing copies. Finally, demonstration that Pong elements have been stably silenced in all strains analyzed indicates that sustained activity of the mPing/Ping family during domestication produced the components necessary for the mPing burst, not the loss of epigenetic regulation.

genomics↗

bioRxiv2018

Is phylogenetic diversity a surrogate for functional diversity across clades and space?

In the face of the biodiversity crisis, it is argued that we should prioritize species in order to capture high functional diversity (FD). Because species traits often reflect shared evolutionary history, many researchers have advocated for a \"phylogenetic gambit\": maximizing phylogenetic diversity (PD) should indirectly capture FD. For the first time, we empirically test this gambit using data from >15,000 vertebrate species and ecologically-relevant traits. Maximizing PD results in an average gain of 18% of FD relative to random choice. However, this average gain hides the fact that in over 1/3 of the comparisons, maximum PD sets contain less FD than randomly chosen sets of species. These results suggest that, while maximizing PD protection can help to protect FD, it represents a risky strategy.\n\nStatement of authorshipFM, MP, MC, SD, GVDR, RG, AOM, CT and WP conceived the design of the study. FM and GVDR conducted the analysis. FM, RG, MP and WP interpreted the results and wrote the first draft of the manuscript. All authors edited the final version.\n\nData accessibility statementMost of the data is publicly available (see methods). The Fish data is available upon request.\n\nCode accessibility statementR functions developed in this paper are available at https://github.com/FloMazel/FD_PD_Max

ecology↗