Adaptive cellular evolution in the intestinal tracts of hyperdiverse African cichlid fishes
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Abstract
Adaptations related to how nutrients are acquired and processed play a central role in the colonization of novel ecological niches and, therefore, in organismal diversification. While the evolution of feeding structures has been studied extensively in this context, the nature of dietary adaptations in the digestive tract remains largely unexplored. Here, we investigate the cellular and molecular basis of dietary adaptations in the massive radiation of cichlid fishes in Lake Tanganyika using comprehensive single-cell transcriptomic data derived from the intestines of 24 endemic cichlid species with distinct habitats and diets. We show that, at the cellular level, dietary adaptations are primarily driven by anterior enterocytes, and that both the relative abundance and gene expression profiles of these cells have evolved in response to rapid dietary specializations. These dietary adaptations are driven by rapidly evolving cell population-specific genes, suggesting that alterations in epithelial cell specification programs and molecular makeup promote ecological diversification.
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We then filtered out non-informative clusters with a median combined mitochondrial and ribosomal fraction higher than 50%
From Figure S1, it seems ddqcR identified a 2-14% mitochondrial UMI contribution threshold for the intestinal cell clusters. How many non-informative clusters with high mitochondrial + ribosomal (<50%) fractions were removed in the subsequent integration and filtering process?
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46.4% - 86.2% of sequencing reads (mean 67.5%) mapped confidently to the reference genome, and 32.5% - 75.6% (mean 52.8%) mapped confidently to the reference transcriptome (Table S2). We obtained a cell / gene count matrix for each sample, which consisted of 1,133-8,226 cells (mean 4,498 cells), with a means of 33,058 reads, 2,255 UMI counts, and 713 detected genes (Figure S1A-C). In total, we detected in each sample between 20,877 and 26,535 genes (mean 24,195 genes).
Does mapping percentage or gene count vary with phylogeny and/or ecology? Put differently, is there any reason to worry that technical variation here might influence your sensitivity for detecting cell type abundance, especially given the low number of replicates per species?
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