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Knit directory: locust-comparative-genomics/

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We aimed to compare the genomes of six Schistocerca species to gain insights into the evolution of their genes since speciation. Specifically, our focus was on investigating whether the three locust species ( S. gregaria, S. cancellata, S. piceifrons) exhibited a similar evolutionary trajectory compared to the grasshopper species ( S. americana, S. serialis cubense, S. nitens). For this, we will be exploring the differences in terms of genes number, content, location, function, expression as well as assessing whether they have undergone selection, duplication, or loss.

We hypothesized that most genes in Schistocerca species are shared but that crucial genes related to locust phase polyphenism must have undergone positive selection. We also supposed that gene families or regulatory elements that are responsive to population density have a different expansion/contraction histories to other genes, thus altering gene dosage and expression levels.

As Schistocerca locusts have shown variation in their behavioral response to high and low density, we further hypothesized that genes with similar function have evolved under positive selection, and that some of these genes originated from ancestral regulatory networks.


sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.3

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Asia/Tokyo
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
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[13] htmltools_0.5.8.1 httpuv_1.6.15     sass_0.4.9        rmarkdown_2.29   
[17] evaluate_1.0.3    jquerylib_0.1.4   tibble_3.2.1      fastmap_1.2.0    
[21] yaml_2.3.10       lifecycle_1.0.4   whisker_0.4.1     stringr_1.5.1    
[25] compiler_4.4.2    fs_1.6.5          Rcpp_1.0.14       pkgconfig_2.0.3  
[29] rstudioapi_0.17.1 later_1.4.1       digest_0.6.37     R6_2.6.1         
[33] pillar_1.10.1     magrittr_2.0.3    bslib_0.9.0       tools_4.4.2      
[37] cachem_1.1.0