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Unraveling geographical modes of speciation processes has been a longstanding topic in biogeography. Divergence can be driven by factors operating on multiple spatial scales, such as geographical distance (isolation by distance, IBD), landscape resistance (isolation by resistance, IBR) and environmental heterogeneity (isolation by environment, IBE). However, it is challenging to assess the relative contributions of such factors, which are usually autocorrelated with each other. On the basis of ~294 K nuclear single‐nucleotide polymorphisms from 53 samples, we integrated population genomics, geographical information and environmental variables to delineate genetic differentiation in the common pheasant Phasianus colchicus across a longitudinal gradient in northern China. Generalized dissimilarity modeling (GDM) was used to analyze the relative importance of IBD, IBR and IBE. We found that the common pheasant in northern China was grouped into six genetic clusters, which was consistent with the taxonomic affinities. Genetic diversity changed along the longitudinal gradient, reaching its lowest level at the eastern edge of the Qinghai–Tibetan Plateau (QTP). The spatial pattern of gene flow suggested that the mountains surrounding the QTP and the mountains in central China have acted as geographical barriers impeding common pheasant dispersal. GDM analysis indicated that environmental heterogeneity is the most important driver explaining the lineage divergence, which supports the IBE model. These results suggest that multiple isolation mechanisms shaped genetic diversity and genomic divergence in this wide‐ranging bird species. Together, our results underscore the importance of leveraging genome‐wide variations and ecological modeling to facilitate a deeper understanding of population divergence processes. [ABSTRACT FROM AUTHOR]

The common pheasant (Phasianus colchicus) in the order Galliformes and the family Phasianidae, has 30 subspecies distributed across its native range in the Palearctic realm and has been introduced to Europe, North America, and Australia. It is an important game bird often subjected to wildlife management as well as a model species to study speciation, biogeography, and local adaptation. However, the genomic resources for the common pheasant are generally lacking. We sequenced a male individual of the subspecies torquatus of the common pheasant with the Illumina HiSeq platform. We obtained 94.88 Gb of usable sequences by filtering out low-quality reads of the raw data generated. This resulted in a 1.02 Gb final assembly, which equals the estimated genome size. BUSCO analysis using chicken as a model showed that 93.3% of genes were complete. The contig N50 and scaffold N50 sizes were 178 kb and 10.2 Mb, respectively. All these indicate that we obtained a high-quality genome assembly. We annotated 16,485 protein-coding genes and 123.3 Mb (12.05% of the genome) of repetitive sequences by ab initio and homology-based prediction. Furthermore, we applied a RAD-sequencing approach for another 45 individuals of seven representative subspecies in China and identified 4,376,351 novel single nucleotide polymorphism (SNPs) markers. Using this unprecedented data set, we uncovered the geographic population structure and genetic introgression among common pheasants in China. Our results provide the first high-quality reference genome for the common pheasant and a valuable genome-wide SNP database for studying population genomics and demographic history. [ABSTRACT FROM AUTHOR]