Qi Fang:
Identification for Genetic Mechanism of Flightlessness in Penguins

Penguins are the only extant birds that have converted their flightless wings for diving and adapted to semi-aquatic environment. This PhD thesis aims to explore the evolutionary puzzle that how penguins lose the flight ability but enhance the underwater flight (flightless wing-propelled diving).

In the first chapter, I compiled a newly developed reference-free whole genome alignment method, Cactus, to align the 363 avian genomes including the penguin lineage. With this alignment, I searched newly derived sequences that evolved specifically in penguin lineage. These newly derived sequences widely distributed across penguin genome, and enriched in long interspersed elements (LINEs) and long terminal repeats (LTRs). I discovered that some of the new sequences inserted in the coding regions of genes with functions such as development of skeleton, muscles, and feathers which might be related to the flightlessness.

In the second chapter, I generated more reliable datasets of orthologs and gene families among 363 avian species including the penguin lineage with the whole genome alignments, and discovered many new gene gain and loss events at the common ancestor of penguins. Based on these data, I was able to further reveal genetic basis of muscle and feather maturation in penguins, which might contribute to their adaption to diving lifestyle.

In the third chapter, I hypothesized that the lineage-specific changes on the regulatory regions might also contribute to the penguin evolution. Therefore, I compared the genomes for all 21 extant penguin species with other bird lineages and investigated the evolutionary patterns of the highly conserved elements (HCEs) in bird genomes.

I specifically looked at those avian HCEs that have showed significantly accelerated evolution in the common ancestor node of all penguin species, the HCEs that have been lost in penguin lineage, and HCEs that specifically appeared only in penguins. Functional analyses indicated that these HCEs include cis-regulatory elements which might regulate the expression of genes that participate in the development of muscle, skeleton and limb, which might also contribute to the penguin evolution. In conclusion, my thesis has reported comprehensive analyses to reveal the genetic mechanisms of flightlessness in penguins at genome-wide level.