Demograhic History And Gene Flow During Silkworm Domestication

Gene flow is a common evolutionary concept that contains all mechanisms causing the migration of genes from a population into another one. It often occurs within a species or between different species. Bottleneck effect, natural selection and genetic drift may play important roles in the evolutionary history of plants and crops. As another evolutionary factor, gene flow may also play an important role in the domestication process of plants and crops. Therefore, the initial studies of demographic history involving gene flow were mainly focused on crop plants. The studies of domesticated animals, although they are crucial for human beings, are lagged behind those of crop plants. Recent published genome-wide datasets based on the next-generation sequencing (NGS) technology allow us to get genetic data more easily to evaluate domestication history of species and the patterns of population divergence process. Well-studied examples include maize, wheat, pigs, chicken, many of which included consideration of demography and introgression. These studies also provide opportunities to study of other model species’ domestication history and the patterns of gene flow. The domesticated silkworm, Bombyx mori, as a model of lepidopteran insects, is domesticated from wild silkworm B. mandarina and is also an economically important insect. However, few similar evolutionary studies have involved in domesticated silkworm, Bombyx mori. Fortunately, increasing genetic data and statistical methods in model species have applied to population genetic studies. In particular, the recently developed approximate Bayesian computation (ABC) method allows use of complicated model in Bayesican framework by providing more detailed knowledge about the demography history and gene flow patterns of species to describe the most likely real domestication scenarios. In the present study, we hypothesized several different models to describe the demographic history of B. mori. In addition, we also evaluated the most possible demographic scenario using the coalescent simulation and ABC method by combining our available non-linked nuclear DNA sequences that are obtained in previous study and our newly sequenced data in a total number of twenty-nine loci. Additionally, we also discussed the introgression pattern based on inferred evolutionary scenario with the goal of understanding the demographic history of silkworm. The main results are below:1. Population genetic analysis and evolutionary analysisIn this study, we have sequenced twelve new genes. The population genetic analyzes of B. mori and its wild silkworm B. mandarina were performed using the software DNAsp Version5.10. We compared the genetic diversity of B. mori and its wild silkworm B. mandarina. The results suggested that the genetic diversity of B. mori is0.017(πtotal) and0.01(θw), which is lower than that of the wild silkworm B. mandarina calculated as0.024(πtotal) and0.026(θW). The domesticated silkworm experienced bottleneck during domestication process. The linkage disequilibriums of B. mori and B. mandarina were also investigated. The results suggested that the linkage disequilibrium of B. mori is higher than that of wild silkworm B. mandarina (0.7448±0.2665Vs0.3948±0.1595). The evolutionary analyzes were performed using three different methods, including maximum likelihood, neighbour-joining as well as Bayesian inference method. The results suggested that phylogenetic tree cannot distinguish different strains of B. mori and B. mandarina sourced from different regions. The clustering relationship is confusing. Population structure analysis further suggested that introgression event might be occurred during the process of silkworm domestication.2. Domestication history of the domesticated silkwormFour model-based evolutionary scenarios to describe the demographic history of B. mori were hypothesized. Using approximate Bayesian computation method, we found that the ’gene flow at bottleneck’ model is the most likely scenario for silkworm domestication. According to this scenario, the starting time of silkworm domestication was estimated to be about7,500years ago; the time of domestication termination was～3,984years ago. The domestication time of B. mori is later than the time of rice domestication (7,500years). The period time of bottleneck is nearly about3,000years. This is consistent with the archeological evidence and results obtained in our previous studies. Importantly, our results also suggested that the gene flow occurred between the domesticated silkworm and its wild relative during the domestication. The domesticated silkworm B. mori might experience sympatric speciation events.3. Gene flow between the domesticated and wild silkwormsTo determine the directional gene flow during bottleneck, MIGRATE3.2.16software and IM software were used to perform coalescent simulation analysis using Bayesian method under our inferred "gene flow at bottleneck" model. We further assumed three directional gene flow scenarios under "gene flow at bottleneck" model. Our coalescent results suggested that the bi-directional gene flow occurred between the domesticated silkworm and its wild relative during the domestication. The migration rate sourced from the domesticated silkworm population into wild silkworm population, is relatively higher than the migrate rate from wild silkworm into domesticated silkworm population. Under the bi-directional gene flow migration model, the relative migration frequency of each locus was also calculated. The simulation results suggested that, when comparing with the two directional migration frequency, twenty-seven loci had a higher migration frequency from the domesticated silkworm into the wild populations than the reverse. The other two genes (mir-2823, Tpk) have the opposite migration trends. Seven silkworm pigment metabolism pathway genes are more likely to migrate from the domesticated silkworm into the wild population. In addition, the introgression from this direction possess higher migration frequency. Besides the bottleneck effect, gene flow may also play important role during silkworm domestication. In addition, the distribution features of population dynamics parameters were also estimated. The results suggested that the domesticated silkworm might compete with wild silkworm population during domestication process.In summary, we not only found that the genetic diversity of the domesticated silkworm was lower than that in wild silkworm but also detected the evidence of bi-directional gene flow between the domesticated silkworm and its wild relative during the domestication process. Such bi-directional gene introgression events may also play an important evolutionary role for the domesticated silkworm to adapt to rearing environments. Additionally, our study may also provide helpful information for understanding the patterns and mechanisms of demographic history and silkworm domestication.