Fig. 3

Correlation of intra-species and inter-species adaptation. A,B Manhattan plots of composite likelihood ratio (CLR) values in RS1 (A) and RS2 (B). C Manhattan plot of CLR values in ZD1 when matched against RS2. Genes residing within the selected regions associated with immune defense, cardiovascular development, and photoreception are labelled by gene names according to their locations. The thin solid black line in each panel denotes the top 1% strongest selective sweep regions. The numbers beneath the horizontal axis indicate the pseudo-chromosomes. D Inhibitory efficiencies of trim35 and trim39-like on SVCV replication in transfected EPC cells measured by the relative abundance of two viral mRNAs, SVCV-N and SVCV-G. The empty vector transfected EPC cells were used as control. *** P < 0.001. E Linear discriminant analysis effect size (LEfSe) is used to classify the microbial community and assess the abundance of taxonomic units associated with each population. The six circles from inside to outside represent different taxonomic levels of the detected bacteria from phylum to species. The colored nodes represent the bacterial taxa that are significantly enriched in the population denoted by the same color (i.e., red for RS1, blue for RS2, and green for ZD1). The nodes in the light yellow indicate no significant difference in the specific taxonomic levels among the compared populations. The bacterial taxa (phylum and class) with differential abundance between the RS1, RS2, and ZD1 populations were shown to the right of the figure. The color square before the classification name denotes the same color-coded population in which the specific bacterial phylum or class is enriched (See Additional file 1: Fig. S16 and Tables S17-18 for detail information). F Reconstructed phylogenetic relationships of ten teleosts (“Methods”: Note 3). The black numbers above each branch refer to the dN/dS ratio. Blue numbers specify the time of divergence between species in millions of years. The geographic time is shown on the top bar. P, Paleocene; E, Eocene; O, Oligocene; M, Miocene; Pli, Pliocene; Ple, Pleistocene. G Significantly over-represented GO biological processes in the C. hamatus genes showing accelerated evolution. The blue circles represent the commonly enriched GO terms in C. hamatus and C. aceratus, while the gold circles represent the GO terms specially enriched in C. hamatus. The sizes of the circles represent the number of genes included in the GO term, with the scale showing in the right corner. The red dashed line indicates a P-value = 0.05. H Morphological and cardiovascular differences between T. bernacchii (representing red-blooded nototheniid) and C. hamatus (white-blooded) that correlated with the fast-evolving biological processes shown in G. (top) The heads of the two fishes showing drastic alterations in overall skull shape, snout length and shape, fin morphology, eye size, and presence/absence of scales. scale bar: 10 mm. (middle) A T. bernacchii (left) and a C. hamatus (right) heart. The sizes are normalized to the body lengths. Scale bar: 10 mm. (bottom) The different colors of the blood from the two fish