Hvilsom C, Qian Y, et. al. (2012) “Extensive X-linked adaptive evolution in central chimpanzees.” PNAS
They analyzed the amount of diversity on autosomes and the X chromosomes in exons in chimpanzees. They showed higher diversity in chimpanzees than in humans, in line with earlier studies. Using the DFE-alpha approach they showed that strong selection (Nes > 100) is slightly elevated on the X chromosome (though they didn’t test for significance, however the Ne of the X should be lower than autosomes, so this is a strong sign of differences in selection). Using two different McDonald-Kreitman based tests they show no evidence for positive selection on autosomes but some on the X chromosome (38% from DFE-alpha). The saw no evidence for selective sweeps in windows in the X chromosome however, they suggest the difference in alpha is caused by fixations of novel recessive mutations being fixed. They also show very reduced coding polymorphism on the X chromosome compared to autosomes, showing faster X evolution caused by positive selection.
Wednesday, June 20, 2012
Monday, June 18, 2012
Robert Summarizes
Drewell RA, Lo N, et. al. (2012) “Kin conflict in insect societies: a new epigenetic perspective.” TREE
Review paper that suggests that imprinting may play a role in conflict between paternal and maternal interests in social insects (i.e. ants, bees, wasps). Since it would be in the paternal interests for workers to produce offspring but this is not in the interests of the queen genes that regulate fertility in workers may be under strong conflict. Since fathers are more related to their own offspring than to a random worker from the (1/2 vs ⅜-0 depending on the matings the queen has), there also may be conflict amongst workers since relatedness is not equal between all workers. However, there seems to be much less methylation in ants than in mammals (3 orders of magnitude less), which indicates that methylation may not play a large role in imprinting, it is mediated by a different mechanism, or that methylation is used much more sparingly. They suggest that there are many candidate genes (primarily developmental and those that control sterility) that are good candidates for imprinting. However, some evidence from behavior of crosses between European honey bees and Africanized bees does indicate that direction of cross affects phenotype.
Doing reciprocal crosses here would be very interesting, but because most queen multiply mate it may complicate matters (or at least make results somewhat not biologically relevant if queens are forced to mate only once). I want to think about this one some more...
Glémin S, Bazin E, and Charlesworth D. (2006) “Impact of mating systems on patterns of sequence polymorphism in flowering plants.” Proc R Soc B
They gathered available sequence data from many plant species and families. They analyzed polymorphism (Watterson’s theta and pi) in synonymous, nonsynonymous, and some non-coding (intronic) sites. They performed ANOVAs to test whether mating system contributed more to diversity levels than other life history traits. Mating system did contribute significantly more than any other trait. They also showed that selfing species have less GC content (possibly due to less biased gene conversion because of low heterozygosity). Additionally they showed tentative evidence that selfers have less effective selection than outcrossers.
Review paper that suggests that imprinting may play a role in conflict between paternal and maternal interests in social insects (i.e. ants, bees, wasps). Since it would be in the paternal interests for workers to produce offspring but this is not in the interests of the queen genes that regulate fertility in workers may be under strong conflict. Since fathers are more related to their own offspring than to a random worker from the (1/2 vs ⅜-0 depending on the matings the queen has), there also may be conflict amongst workers since relatedness is not equal between all workers. However, there seems to be much less methylation in ants than in mammals (3 orders of magnitude less), which indicates that methylation may not play a large role in imprinting, it is mediated by a different mechanism, or that methylation is used much more sparingly. They suggest that there are many candidate genes (primarily developmental and those that control sterility) that are good candidates for imprinting. However, some evidence from behavior of crosses between European honey bees and Africanized bees does indicate that direction of cross affects phenotype.
Doing reciprocal crosses here would be very interesting, but because most queen multiply mate it may complicate matters (or at least make results somewhat not biologically relevant if queens are forced to mate only once). I want to think about this one some more...
Glémin S, Bazin E, and Charlesworth D. (2006) “Impact of mating systems on patterns of sequence polymorphism in flowering plants.” Proc R Soc B
They gathered available sequence data from many plant species and families. They analyzed polymorphism (Watterson’s theta and pi) in synonymous, nonsynonymous, and some non-coding (intronic) sites. They performed ANOVAs to test whether mating system contributed more to diversity levels than other life history traits. Mating system did contribute significantly more than any other trait. They also showed that selfing species have less GC content (possibly due to less biased gene conversion because of low heterozygosity). Additionally they showed tentative evidence that selfers have less effective selection than outcrossers.
Friday, June 15, 2012
Robert Summarizes
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.
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.
Robert reawakens the blog?
I've decided to get better at summarizing my readings for a few reasons. First, I'm terrible at remembering what I've read, so if I write something about it that should improve. Second, I need to get better at names, and writing authors names after I read something will help that. Lastly, I think it (or your people) will guilt me into reading more effectively.
I was going to set up a new blog for to do this or just use a google doc, but since we aren't using this blog for anything else, and this way you two can bug me to complete this, I figured that I'm gonna use E(h)volution, barring objections. I'm aiming for my summaries to be 100-200 words, with perhaps a bit of opinion about the work. It would be awesome to have little mini discussions about the articles here (think baby journal club), especially if you think I've summarized something incorrectly, or missed the point. I want to do these on a semi-daily basis, usually one or a few articles. You have my permission to yell at me if I haven't done one for a while. Next post with a few from the last couple days follows.
Cheers!
Robert
I was going to set up a new blog for to do this or just use a google doc, but since we aren't using this blog for anything else, and this way you two can bug me to complete this, I figured that I'm gonna use E(h)volution, barring objections. I'm aiming for my summaries to be 100-200 words, with perhaps a bit of opinion about the work. It would be awesome to have little mini discussions about the articles here (think baby journal club), especially if you think I've summarized something incorrectly, or missed the point. I want to do these on a semi-daily basis, usually one or a few articles. You have my permission to yell at me if I haven't done one for a while. Next post with a few from the last couple days follows.
Cheers!
Robert
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