Carneiro M, Albert FW, et. al. (2012) “Evidence for widespread positive and purifying selection across the European rabbit (Oryctolagus cuniculus) genome.” Mol Biol Evol.
They extracted RNA from rabbit brains of 2 species and assembled the transcriptome then quantifies both positive and negative selection. They used several methods for alpha (including DFE-alpha) and got very high estimates of positive selection, alpha was ~0.6. They found very high estimates of negative selection as well, at least 93% of sites had Nes > 10. They found slightly increased selection on the X chromosome in one species, but not in the other, neither of these comparisons to autosomes was significant though. They attribute most of this increased selection to very large Ne in rabbits (~ 800,000 - 1,130,000 for the two species).
He F, Zhang X, et. al. (2012) “Genome-wide analysis of cis-regulatory divergence between species in the Arabidopsis genus.” MBE.
The authors looked at expression in F1s between thaliana (materna) and lyrata (paternal). They found lots of allele specific expression (ASE). Most genes that showed ASE (up to ~90%) only from the A. lyrata copy. They found that A. lyrata ASE genes were enriched for a marker associated with repression during development, while the ASE A. thaliana genes were associated with a different marker associated with increased growth during development. They suggest imprinting is unlikely due to the small number of imprinted genes found in A. thaliana. This argument seems weak, since there still could be more imprinted loci we don't know about, and there shouldn't be many in selfers anyway. Another explanation would be accumulation of deleterious alleles in the selfer that are recessive, so the outcrossing allele is preferentially expressed.
Hufford MD, Xu X, et. al. (2012) “Comparative population genomics of maize domestication and improvement.” Nat. Genet.
They compared wild, domesticated, and “improved” maize genetics. They found lots of sweeps in domestication, and in improvement, but with lower signals of sweeps in improvement. The number of sites and genes acted on in improvement seems much smaller. Looks like mostly regulatory changes though. pi ~= .004, domesticated races kept most of wild diversity.
Hey Robert! Did Carneiro et al. account for biases due to expression level (it's easier to detect polymorphism in high expression genes, which are also expected to be under stronger purifying selection). Also, how did they get divergence for calculating alpha?
ReplyDeleteThey looked at how gene expression level (in FPKM, which probably makes more sense to you than to me) affected both negative and positive selection. They found that higher expressed genes were more constrained, and showed both more positive and negative selection.
DeleteThey calculated divergence from the alignment of a pool of DNA from several Iberian hares to the genome they used. Just counted up the number of sites that differed, it looks like