Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions^1–3. Here we address these issues by analysing the genomes of 363 bird species⁴ (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous–Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous–Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.

The ground tit (Parus humilis) is endemic to the Tibetan plateau. It is a member of family Paridae but it was long thought to be related to the ground jays because of their morphological similarities. Here we present the ground tit’s genome and re-sequence two tits and one ground jay, to clarify this controversially taxonomic status and uncover its genetic adaptations to the Tibetan plateau. Our results show that ground tit groups with two tits and it diverges from them between 7.7 and 9.9 Mya. Compared with other avian genomes, ground tit shows expansion in genes linked to energy metabolism and contractions in genes involved in immune and olfactory perception. We also found positively selected and rapidly evolving genes in hypoxia response and skeletal development. These results indicated that ground tit evolves basic strategies and ‘tit-to-jay’ change for coping with the life in an extreme environment.

The Qinghai-Tibet Plateau (QTP) is well known for being of great importance in the evolution of montane species due to its unique geological history and landform configuration, climate complexity, and diversified habitats. The effect of environmental changes since the Quaternary on species diversification, population genetic structure, and demography under environmental change can be studied using phylogenetic and phylogeographical approaches. Birds are the most well-studied group of all terrestrial vertebrates with regard to their response to climatic changes over time. Herein, we briefly review the species diversification of birds in response to the uplift of the QTP, focusing on summarizing the different phylogeographical patterns of birds on the Plateau, its southeastern margin, and the Eastern Himalayas and the reasons underlying these patterns. Speciation was found to be closely related to the uplift of the QTP, with different patterns of intraspecific processes: (1) no divergence within a single refuge was identified in a restricted semi-continuous area of the eastern margin of the Plateau; (2) two divergent lineages with separated refugia were located at the south-eastern and north-eastern margins of the plateau; and (3) multiple divergent lineages within subregions were found in the Eastern Himalayas. Glacial movements and induced climate change are considered to be key factors in shaping these different patterns. The species distributed mainly in the heavily ice-covered platform regions of the Plateau experienced population expansion following the retreat of the extensive glaciations, whereas the species distributed on the ice-free edges of the plateau maintained their population size at a stable level. Demographic stresses on the edge species might have been mitigated by the milder climate in comparison to their platform-distributed counterparts. Various behavioral and ecological characteristics, including dispersal capacity, habitat preference, and elevation specificity, along with evolutionary history might have helped to shape these different phylogeographical patterns.

When different species experience similar selection pressures, the probability of evolving similar adaptive solutions may be influenced by legacies of evolutionary history, such as lineage-specific changes in genetic background. Here we test for adaptive convergence in hemoglobin (Hb) function among high-altitude passerine birds that are native to the Qinghai-Tibet Plateau, and we examine whether convergent increases in Hb–O ₂ affinity have a similar molecular basis in different species. We documented that high-altitude parid and aegithalid species from the Qinghai-Tibet Plateau have evolved derived increases in Hb–O ₂ affinity in comparison with their closest lowland relatives in East Asia. However, convergent increases in Hb–O ₂ affinity and convergence in underlying functional mechanisms were seldom attributable to the same amino acid substitutions in different species. Using ancestral protein resurrection and site-directed mutagenesis, we experimentally confirmed two cases in which parallel substitutions contributed to convergent increases in Hb–O ₂ affinity in codistributed high-altitude species. In one case involving the ground tit ( Parus humilis ) and gray-crested tit ( Lophophanes dichrous ), parallel amino acid replacements with affinity-enhancing effects were attributable to nonsynonymous substitutions at a CpG dinucleotide, suggesting a possible role for mutation bias in promoting recurrent changes at the same site. Overall, most altitude-related changes in Hb function were caused by divergent amino acid substitutions, and a select few were caused by parallel substitutions that produced similar phenotypic effects on the divergent genetic backgrounds of different species.