The outbreak of highly pathogenic avian influenza (HPAI) H5N1 disease has led to significant loss of poultry and wild life and case fatality rates in humans of 60%. Wild birds are natural hosts for all avian influenza virus subtypes and over120 bird species have been reported with evidence of H5N1 infection. Influenza A viruses possess a segmented RNA genome and are characterized by frequently occurring genetic reassortment events, which play a very important role in virus evolution and the spread of novel gene constellations in immunologically naïve human and animal populations. Phylogenetic analysis of whole genome or sub-genomic sequences is a standard means for delineating genetic variation, novel reassortment events, and surveillance to trace the global transmission pathways. In this paper, special emphasis is given to the transmission and circulation of H5N1 among wild life populations, and to the reassortment events that are associated with inter-host transmission of the H5N1 viruses when they infect different hosts, such as birds, pigs and humans. In addition, we review the inter-subtype reassortment of the viral segments encoding inner proteins between the H5N1 viruses and viruses of other subtypes, such as H9N2 and H6N1. Finally, we highlight the usefulness of genomic sequences in molecular epidemiological analysis of HPAI H5N1 and the technical limitations in existing analytical methods that hinder them from playing a greater role in virological research.

Adaptive convergent evolution, which refers to the same or similar phenotypes produced by species from independent lineages under similar selective pressures, has been widely examined for a long time. Accumulating studies on the adaptive convergent evolution have been reported from many different perspectives (cellular, anatomical, morphological, physiological, biochemical, and behavioral). Recent advances in the genomic technologies have demonstrated that adaptive convergence can arise from specific genetic mechanisms in different hierarchies, ranging from the same nucleotide or amino acid substitutions to the biological functions or pathways. Among these genetic mechanisms, the same amino acid changes in protein-coding genes play an important role in adaptive phenotypic convergence. Methods for detecting adaptive convergence at the protein sequence level have been constantly debated and developed. Here, we review recent progress on using genomic approaches to evaluate the genetic mechanisms of adaptive convergent evolution, summarize the research methods for identifying adaptive amino acid convergence, and discuss the future perspectives for researching adaptive convergent evolu-tion.

Genomic data are important for understanding the origin and evolution of traits. Under the context of rapidly developing of sequencing technologies and more widely available genome sequences, researchers are able to study evolutionary mechanisms of traits via comparative genomic methods. Compared with other vertebrates, bird genomes are relatively small and exhibit conserved synteny with few repetitive elements, which makes them suitable for evolutionary studies. Increasing genomic progress has been reported on the evolution of powered flight, body size variation, beak morphology, plumage colouration, high-elevation colonization, migration, and vocalization. By summarizing previous studies, we demonstrate the genetic bases of trait evolution, highlighting the roles of small-scale sequence variation, genomic structural variation, and changes in gene interaction networks. We suggest that future studies should focus on improving the quality of reference genomes, exploring the evolution of regulatory elements and networks, and combining genomic data with morphological, ecological, behavioural, and developmental biology data.