Nucleotide Diversity, Selection Signature And Domestication History Of Silkworm, Bombyx Mori

Domestication is a kind of rapid adaptive evolution resulted from dramatic environmental alteration in short time. The major driven force is so called "bottleneck". During domestication, people only chose a small part of individuals in ancestor population to raise and domesticate and resulted in reduction of effective population and genome-wide loss of diversity in domesticated species. In addition, natural or artificial selection, population extension and subdivision can often have impact on the domesticated species and signatures of such driven force were left in the genome.Domesticated silkworm, Bombyx mori, originated from ancient Chinese wild silkworm, Bombyx mandarina. While domesticated silkworm has experienced a history of artificial selection and adapted to man-made environment, wild silkworm currently occurs in mulberry fields. B. mori and B. mandarina differ in many traits including growth rate, flight behavior, egg laying, cocoon size, silk quality, and a kind of mimicry as a result of domestication. This provides us with a good opportunity for studying on genetics and molecular evolution using silkworm as model organism. Moreover, as the unique domesticated insect and model organism in Lepidoptera with abundant genetic resources, it's necessary to study effects of different driven forces during domestication and such studies will facilitate the breeding and utilization of genetic resources of silkworm.There have been many intensive studies on molecular mechanism of domestication of crops including maize, rice, wheat and barley. However, there are a few studies on silkworm domestication. In this study, we sequenced 10 genes of both domesticated and wild silkworms using traditional method and investigated patterns of domesticated silkworm through diversity analysis, neutrality tests, phylogenetic analysis, linkage disequilibrium analysis and coalescent simulation. The major conclusions were given below:1. Diversity of silkwormWith the sequence data of 10 loci sequenced in this study, it was found that nucleotide diversity in domesticated silkworm was significantly reduced compared to that in wild silkworm. The polymorphism parameters were 0.01049 (πtotal) or 0.01011 (θW) in domesticated silkworm and 0.01641 (πtotal) or 0.02041 (θW) in wild silkworm. By contrast, the loss of diversity in domesticated silkworm was 36.1(πtotal) or 50.4% (θW) during domestication, which is similar to the loss levels found in major cultivated crops. Two of ten loci (DefA and HATPS) showed dramatic loss of diversity between domesticated and wild silkworm. Given that HATPS was target of selection, DefA may be a candidate of selection.2. Neutrality testsTajima's D tests were performed for 10 loci. Average D value of domesticated silkworm was higher than that of wild silkworm, indicating a recent expansion in domesticated silkworm, which was the case in crops. Three of ten loci showed significant D values (AchE, ER and DefA). MK test and HKA test were not significant for all loci, possibly because the B. mori and B. mandarina are closely related species and there is a little divergence between the two species. The power of multilocus HKA and MK test is low.3. Phylogenetic analysis and linkage disequilibrium analysisAmong 10 loci, only phylogenetic trees based on DefA and HATPS can distinguish domesticated and wild silkworms. Similarly, linkage disequilibrium analysis suggested that DefA and HATPS have the same pattern, that is, linkage disequilibrium curves did not exist for domesticated silkworm but did exist for wild silkworm. The same pattern of phylogeny and linkage disequilibrium also supported that DefA may be a candidate of selection.4. Bottleneck model of domestication for domesticated silkworm and target of selectionCoalescent simulations based on maximum likelihood method were performed in order to either assessing bottleneck effect during domestication or performing likelihood ratio tests for detecting target of selection. The bottleneck parameter (k) of domesticated silkworm was 1.5, suggesting that silkworm experienced more severe bottleneck than crops. Based on analysis of likelihood curves and likelihood ratio tests, I can conclude that only DefA and HATPS were target of selection and other 8 loci evolved neutrally.5. Domestication history of domesticated silkwormBottleneck models representing evolutionary history of domesticated and wild silkworms were set up using coalescent simulations based on Bayes method. In conclusion, domestication history of domesticated silkworm is consistent with sympatric model. It means that domestication of silkworm began 7000 years ago and ended 5000 years ago and gene flow between domesticated and wild silkworm prevailed during domestication. In addition, I also assessed two coalescent simulation methods in this study. Simulation based on maximum likelihood method was convenient and time-saving, it's better to use this simulation to assess bottleneck intensity and detect target of selection. By contrast, simulation based on Bayes method was complex and major factors of domestication were included in this model. Thus it's better to study on evolutionary history of domesticated species by Bayesian method.