Characterization of genomic biodiversity through comprehensive species sampling has the potential to revolutionize our understanding of macroevolution, which focus on the patterns of biodiversity over time and space. Comparative genomics across long evolution timescale have brought new insights on building the link between the change in molecular level and the evolution of global biodiversity. I will give some examples to show how phylogenomics and comparative genomics analyses have the potential to overcome the challenges in connecting microevolution and macroevolution. Resolving the phylogeny for species experienced rapid radiation in ancestral stage such as bird class has long been a challenge in systemic biology. We proposed to utilize full genome data in phylogenetic analyses, which have been confirmed very successful and have produced a highly supported avian order phylogeny that resolves many debates on the timing and topology of their radiation. The new avian phylogenic tree has changed our view of the evolutionary process of many avian life-history traits. Whole genome comparison for all bird species with other vertebrate species revealed several distinct macroevolution patterns of avian genome. Different with other animal lineages that develop evolutionary innovation by obtaining new genetic materials, the bird genomes have extremely low new gene born rate. Instead, our studies suggest the bird genomes obtain millions of elements that specifically only conserved in bird lineages that can modify the expression patterns of the associated genes leading to the development of key avian trait innovations.