Tempo of avian chromosome evolution. (A–D) Genomic synteny between green sea turtle, rattlesnake, American alligator versus emu and green sea turtle versus golden eagle, respectively. Chromosome names with blue/red color denote the fused chromosomes in reptiles and the homologous chromosomes of emu, respectively. Each chromosome is indicated by the first letter of species name and chromosome number. (E) Chromosomal rearrangements across all major phylogenetic branches of birds. The phylogenetic branches (Jarvis et al. 2014; Claramunt and Cracraft 2015) are color-coded according to the respective average rate of intrachromosomal changes, and the numbers with different colors indicate those of detected chromosomal fissions (red) and fusions (blue). The intrachromosomal rearrangement number per chromosome of birds compared to sea turtle is shown in the heat map with a different color scale for macro- and microchromosomes, given their drastically different size and rearrangement numbers. (F) Paleognaths show more rearrangements per chromosome than neognaths. (***) P < 0.0005. (G) Microchromosomes have a higher rearrangement number per 10 Mb length than macrochromosomes. (***) P < 0.0005. (H) The distributions of the length ratios of syntenic blocks comparing turtle versus emu across different types of genomic regions, which indicate that the major source of sequence loss in birds is from repeat regions. (I) The outer dot plot shows the correlation between the overall turtle versus emu syntenic length ratio per chromosome versus the size of the chromosome (blue for microchromosomes, red for macrochromosomes). The size of the dots is scaled to the average GC content of each chromosome. The inner plot shows the positive correlation between GC content and turtle versus emu syntenic length ratio. Each dot represents one syntenic block, with the red ones for the macrochromosome blocks and the blue ones for the microchromosome blocks. (J) Microchromosomes have higher turtle versus birds syntenic length ratios than macrochromosomes, suggesting that microchromosomes experienced more severe sequence loss in birds.
