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Several studies have shown that genomic features of independent secondary contact zones are variable (Nolte et al. The outcomes of the resulting interplay between allopatric populations have improved our understanding of the process through which geographic isolation promotes biodiversity (April et al. Therefore, many genetic studies have been performed on secondary contact zones to investigate their evolutionary outcomes, including genomic and phenotypic features of hybrids (Jiggins and Mallet 2000 Nolte et al. The resulting hybrids and gene introgression are subject to natural selective pressures, including endogenous (genetic incompatibility) and exogenous selection (natural selection). In contrast, if reproductive isolation (pre- or post-zygotic isolation) is not completed between populations, hybridization will occur in a secondary zone. Geographic isolation is the most commonly accepted cause of genetic divergence between populations, and can sometimes lead to new species with distinct phenotypes (Coyne and Orr 2004). Collectively, our results demonstrated that genomic and phenotypic consequences of secondary contact varied in marine variable environments. Moreover, the body size changes in the introgressed populations possibly affect the introgression patterns of mitochondrial genomes across these zones. Actually, we observed biased introgression of a candidate gene, neuropeptide Y ( NPY), which potentially controls body size in the ice goby. On phenotype analyses, vertebral numbers were clearly explained by nuclear genomic ancestry in both secondary contact zones, whereas body size was not, suggesting that a little introgression of nuclear genes regulates body size. Population genetic analyses revealed asymmetric introgression of the mitochondrial genome of either lineage relative to little admixture of nuclear genomes in both secondary contact zones. Herein, we performed integrated analyses of genotypes and phenotypes of two independent secondary contact zones and investigated their consequences. In particular, populations in the Japan Sea have a larger body size and numbers of vertebrae than those in the Pacific Ocean. Populations of the ice goby Leucopsarion petersii are distributed throughout the Japanese archipelago and comprise genetically and phenotypically divergent groups in the Japan Sea and the Pacific Ocean. Size = 0.9, linetype = 4, colour = pcgrr::color_palette]])ġ9 File: value_boxes.Genetic and phenotypic analyses of independent secondary contact zones between certain pairs of divergent populations offer powerful opportunities to assess whether the consequences vary with different environmental backgrounds. Size = 14)) + ggplot2::geom_hline(yintercept = as.numeric(tmb_estimate), Size = 16, vjust = -1.5), = ggplot2::element_text(family = 'Helvetica', Size = 14), = ggplot2::element_text(family = 'Helvetica', Ggplot2::theme(legend.title = ggplot2::element_blank(),Ī = ggplot2::element_blank(), legend.position = 'none',Ī = ggplot2::element_text(family = 'Helvetica', Ggplot2::xlab('Primary Site') + ggplot2::ylab('Tumor mutational burden (mutations/mb)') + Ggplot2::scale_fill_manual(values = tmb_site_color_vec) +

Tmb_log10, FUN = median), y = tmb, fill = primary_site)) + Tmb_plot_site < - ggplot2::ggplot(data = tcga_tmb) + ggplot2::geom_boxplot(mapping = ggplot2::aes(x = reorder(primary_site, Tcga_tmb % dplyr::filter(!is.na(primary_site)) %>%ĭplyr::select(primary_site, tmb_ns_log10, tmb_ns) %>%ĭplyr::rename(tmb = tmb_ns, tmb_log10 = tmb_ns_log10) Tmb_site_colors$color % dplyr::filter(!is.na(primary_site)) %>%ĭplyr::select(primary_site, tmb_log10, tmb) Plot_tmb_primary_site_tcga % dplyr::filter(!is.na(primary_site))

#Genodive manual license#

19 File: mutational_burden.R, author: sigven, license: MIT License