Clonal evolution of a tumor ecosystem depends on different selection pressures that are principally immune and treatment mediated. We integrate RNA-seq, DNA sequencing, TCRseq and SNP array data across multiple regions of liver cancer specimens to map spatio-temporal interactions between cancer and immune cells. We investigate how these interactions reflect intra-tumor heterogeneity (ITH) by correlating regional neo-epitope and viral antigen burden with the regional adaptive immune response. Regional expression of passenger mutations dominantly recruits adaptive responses as opposed to hepatitis B virus and cancer-testis antigens. We detect different clonal expansion of the adaptive immune system in distant regions of the same tumor. An ITH-based gene signature improves singlebiopsy patient survival predictions and an expression survey of 38,553 single cells across 7 regions of 2 patients further reveals heterogeneity in liver cancer. These data quantify transcriptomic ITH and how the different components of the HCC ecosystem interact during cancer evolution.

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Arabuko Sokoke Forest (ASF) is the largest area of coastal forest remaining in East Africa and a major Important Bird Area in mainland Kenya. The study analysed data from point count surveys over 15 months in three land use types; primary forest (PF), plantation forest (PL), and farmlands (FM), and compared these to the first comprehensive bird checklist for the forest, as well as recent surveys from other studies.  Avifaunal diversity and abundance were compared using multivariate analysis to determine bird responses to different land use characteristics. The primary forest held a distinctive bird community, while the bird communities of farmlands and plantation forest were more similar to each other. Land use had a significant effect on overall avian diversity and abundance. The current forest avifauna was divided into forest specialists (16 species), forest generalists (26 species) and forest visitors (30 species).   Seven species of forest specialist and generalists recorded prior to 1980 may no longer occur in the forest.  Of 38 specialists and generalists recorded in our point counts, 19 were also recorded on farmland and 28 in plantations.  One forest specialist, the Green Barbet, was most encountered outside the forest.  Future research should focus on habitat use by these bird species, and the extent of movement by forest birds between the remaining patches of coastal forest. Patterns of habitat use by birds in the area suggest that vegetation heterogeneity and habitat complexity are especially significant in sustaining diverse and abundant bird populations. The management of plantations and farmland will be critical for the conservation of forest generalists and forest visitors.